Please understand that all cue information in this list is arranged to reflect current availability in different media.  Therefore, some things are listed as, say, three cues on this list because they are available in three different locations.  However, these same three cues may very well have been recorded as one big one in the original score.

00:00-00:20 Fox Fanfare
I have no idea which version was used in the film, but for my own purposes I have selected the version from the Return of the Jedi Special Edition Soundtrack on RCA/Victor.

00:26-02:10 Main Title/Arrival at Naboo
This cue matches the SONY album from 0:00-1:48, containing the Star Wars Main Title and the opening moments of the “Arrival at Naboo”.  However, at 1:51 the album segues into music written for the “Arrival at Coruscant”, which finishes out track 1 of that CD.

02:10-03:30 Aboard the Federation Battleship
Instead of crossfading into the Coruscant material, the track “sqtense2.imc” on the TPM CD-ROM continues into true “Arrival at Naboo” music, providing over two minutes of score, accompanying (a) the scenes with TC-14, and (b) the two Jedi as they discuss negotiations and look out the window.

03:30-04:52 Nemoidians/The Jedi Wait/Darth Sidious
The first two parts of this cue are heard in "sqtense2.imc", (c) the introduction of the Nemoidians, and (d) TC-14 bringing the Jedi some drinks, while the Darth Sidious material can be heard in the TPM CD-ROM as “sqeerie.imc”  A note about the whispering choir motif used throughout the film, and first heard here:  I believe it was recorded as a separate element from the actual cues, and dropped in at the discretion of George Lucas and/or Ken Wannberg during the final mixing process.  UPDATE:  I have been told that the Darth Sidious material in this cue does not match the movie, and that the version in the film remains unreleased.  I have not had a chance to double check this info yet.

04:52-05:05 Destroying the Republic Ship/The Gas
Heard, with minimal sound effects, on TPM CD-ROM as the closing moments of “sqfedshipintrocs.imc”, this short bit of music accompanies the shots of the Nemiodians blowing up the Republic Cruiser that brought the Jedi to Naboo, and the first moments of the following scene as TC-14 drops the tray and the Jedi spring to action, lightsabers drawn.

05:05-05:33 "Dioxisin!"  NOW AVAILABLE
This material has been made available in the recently released "Jedi Power Battles" game for Sony Playstation.  The last note, however, a sustained string note, remains unreleased.

05:33-07:09 Jedi Fight
This cue can be found as “sqdroidfightloop.imc” on the TPM CD-ROM.  It is a deftly written piece of action music that accompanies the two Jedi as they fight Battledroids with their lightsabers and attempt to reach the bridge of the Federation Battleship.  Especially exciting is the powerful rendition of the Force Theme as Qui-Gon Jinn cuts through the blast doors with his lightsaber. UPDATE:  The music previous thought to be unreleased has come to light as a tracked portion of "They Will Kill You If You Stay", recently released in the "Jedi Power Battles" game for Sony Playstation.  This music is low and somber and accompanies the scene on the bridge where Rune Haako tells Nute Gunray “We will not survive this…”.  We then resume with music available in the game.  The ending of the cue is found in “sqdroidfightend.imc”.

07:09-08:39 Amidala Confronts The Nemoidians
At this point, we segue back to music found on the SONY CD, specifically track 13 at 2:52-4:23.  It accompanies the scene where Queen Amidala contacts Nute Gunray and tells him the Federation has gone too far.  After an orchestral swell and melodic statement by ethnic flute, the score segues to the next cue.

08:39-09:30 Message from Palpatine (part 1)
Edited out of the SONY album, this passage features solo bassoon in some great melodic turns, and can be found in the TPM CD-ROM as “sqtheed.imc”.  After about a minute, it segues back into the SONY album.

Message from Palpatine (part 2)
The SONY CD picks up again with track 13 from 4:23-4:51, the end of the track.  On the album, this music tails out, but in the film it directly segues in an exciting fashion with the next cue.  (*NOTE:  this cue is reprised in the film to accompany the moments where the Gungans fire up their shield generator.)

09:30-10:18 The Invasion Begins
This cue, which first presents the militaristic theme for the Trade Federation and the Battledroids, can be heard on the SONY CD as part of track 14, running from 1:05-1:44.  There is an “alternate” version found on the TPM CD-ROM, which is this same performance with the addition of a timpani/snare roll inro and a stripped-down reprise of the march theme.  This “alternate” also has a looped fade out which was made by the makers of the video game and is not how the cue was written by Williams.  In the film, this cue sneaks out with an edit to a brassy chord, which can be heard on TPM CD-ROM as file “sqdanger1.imc”, although this file also has extra introductory percussion that was edited out of the film.  This cue effectively brings to an end ten minutes of uninterrupted music in the film.  A clean ending can be heard in track 8 of the music from "Jedi Power Battles" for Sony Playstation.

(10:18 - ???) Omitted Action Music
There is a theory going around the internet that music which appears on the SONY CD  track 14, from 2:08-2:47 was originally intended to segue directly from the end of the previous cue, in place of the edit to "sqdanger1.imc".  This is supported by the cue's placement on the SONY CD immediately following the previous cue, as well as an appearance in the EPISODE 1 INSIDER'S GUIDE, where it is also edited to follow the previous cue.  The most complete version of this piece can be found on the TPM CD-ROM GAME as  “sqfight5.imc”.  According to the screenplay, cut-scenes from the TPM GAME, and clips from a making of special, there was a sequence where Obi-Wan was seen emerging from the Naboo Swamp, "Apocalypse Now"-style and it's possible that this music may have been written for this sequence and continued into the scene where Qui-Gon collides with Jar Jar as he flees the giant troop transports.

(11:27-12:36) Jar Jar Binks
Another cue to be written for the film but ultimately unused, this music serves as an introduction to Jar Jar Binks and is titled as such on the the CD, where it is featured as track 4, 0:00-1:08.  In the film, this music would start just after Qui-Gon explains to Obi-Wan that Jar Jar is “a local”;  we then cut to the Jedi running through the forest, Jar Jar running behind them, shouting “Ex-squeeze me!”.  The flourish approximately one minute in matches the moment where Jar Jar spins around and almost hits Obi-Wan with his ears.  In the film, the cue fades in during the musical flourish at 1:08 as Jar Jar makes his funny scream and jumps in the water.

12:36-13:31 Otoh Gunga
This cue is on the CD as track 4, from 1:08 to 2:05.  The repeating flute figure at 2:05 can be found without the SONY overlap as the end of “sqgungaintro.imc” on TPM CD-ROM.

13:31-17:55 Boss Nass/The Bongo (part 1)
One of the few accurate presentations of a cue on the SONY album, this music appears as track 10, starting at 0:00 and running until 4:39, the end of the track.  It begins with the Jedi and Jar Jar entering Otoh Gunga through the waterproof membrane, and continues through the meeting with Boss Nass and the first segment of the Bongo trip, finishing as our heroes narrowly avoid being devoured by a sea creature.

17:58-18:57 Darth Sidious II/The Bongo (part 2)
The Nemoidians once again speak with Darth Sidious and the music that accompanies this sequence can be found on the SONY CD, track 14, starting at 3:45.  We then return to the Jedi and Jar Jar in the Bongo, where they run out of power.  The music for this segment follows the Sidious material on track 14 of the CD, running until 4:57, although it is shortened quite a bit in the movie.  On CD, the closing chord, which accentuates the Bongo’s loss of power, crossfades into the string ostinato motif from “Duel of the Fates”, which does not occur in the film.  A version with a clean ending can be found in the TPM CD-ROM, in file “sqsidiousmood.imc”.

19:08-19:47 The Bongo (part 3)
After restoring power to the Bongo, our heroes again encounter threatening sea creatures. In the film, the cue starts with the music at 2:08, which occurs immediately after they restore power and Jar Jar screams at the monster outside the window.  The music continues without interruption into the next cue.

19:47-20:23 "Ah, victory…"
A second presentation of the military music for the Federation Droid Army, this track is available on the SONY CD, number 14, from 2:47 to 3:20.  The end of this cue on the CD segues into some unused synth music that obliquely resembles whale calls, but a clean ending can be heard in the TPM CD-ROM, “sqfedannounce.imc”.

20:23-20:41 "Dis'n loverly…" Unreleased
Here we find only the third instance in the first 20 minutes or so of score that is currently unavailable in any form (except the movie itself, of course).  This short piece connects the end of the previous cue with the beginning of the next, and is distinguished by some lovely pastoral reed phrases that musically mirror the sentiments of Jar Jar regarding the city of Theed.

20:41-21:45 Captured Queen
The Nemoidians have captured the Queen and her handmaidens and lead them down the stairs of the palace.  This is available on the TPM CD-ROM as file “sqtheedstalk.imc”.  It segues directly into the next cue.

21:45-22:28 Bombad Jedi
Jar Jar and the Jedi spring into action and rescue the Queen and her entourage from the Battledroids in this exciting cue. This cue, found as file “sqtheedattack.imc” on the TPM CD-ROM, continues through the brief conversation in the courtyard and ends when our heroes reach the door to the hangar.

22:28-23:37 "They will kill you if you stay…" NOW AVAILABLE
This cue is an energetic piece of music that underscores the conversation outside the hangar door as the Queen decides to go to Coruscant with the Jedi.  It continues with some nice “rallying” string writing as Qui-Gon confronts the Battledroid and Obi-Wan walks to the captured pilots.

23:37-24:05 Freeing the Pilots
Now everyone springs into action in a nice action set-piece, scored with brass as the group make their escape from Naboo.  This first segment is heard on the SONY CD, track 12, 2:40-3:23.  The timpani figures at the end directly overlap the opening note of the next cue.  There is a version on the EPISODE 1:RACER CD-ROM, "escapeloop.wav", that contains a clean opening of the track.

24:05-24:44 Escape from Naboo
Found as file “sqfight1.imc” on the TPM CD-ROM, this cue presents the action motif used for the escape from Naboo, which will be continued into the next cue.  Additionally, this cue and most of the next one are tracked into the Podrace as Anakin refires his malfunctioning pod and defeats Sebulba.

24:44-25:56 The Heroics of Artoo-Detoo
It is during this cue that we are introduced to the resourceful little droid, Artoo-Detoo.  A nice musical touch by John Williams is the exotic phrase in the bassoon at the end of the cue, accompanied by finger cymbals, that conveys the desert-y feel of Tatooine and the Hutts.  This cue can be heard from 0:13-1:29, track 15, SONY CD.  Much of it was also tracked into the podrace sequence.

25:56-26:09 To Tatooine Unreleased
This short segment of music underscore the conversation between Panaka and the Jedi as they argue about taking the ship to Tatooine for repairs.

26:09-26:51  Darth Sidious and Maul NOW AVAILABLE
We return to the Federation ship, where the Nemoidians must explain their failure to capture the queen to Darth Sidious.  Not satisfied by their incompetence, Sidious reveals his apprentice, Darth Maul, and sets him the task of capturing the Queen.  This cue consists primarily of Sidious’ theme, with the whispered choral motif appearing as Maul is revealed (overdubbed by Ken Wannberg and Lucas, I believe).  After Sidious ends the transmission, the Nemoidians nervously discuss their situation, and Maul’s sinister theme is heard in the low wind section.  This cue is about 55 second long and can be heard in the "Jedi Power Battles" game for Sony Playstation track 2 section "c".

26:51-27:04 The Queen's Ship
Actually the end of the previous cue, this short segment is the portion currently available, on the TPM CD-ROM, “sqscary1.imc”.  It tails out as Panaka introduces the Queen to Artoo-Detoo.

27:45-28:40 Padme and Jar Jar/Tatooine
In the final film, this is the first presentation of Jar Jar’s theme, since the earlier scoring was discarded during mixing.  After his theme, the score swells into some wonderful chords that accompany the arrival of the group at Tatooine, nexus of events in the Star Wars saga.  A powerful french horn figure scores the ship’s landing.  This cue is on the SONY CD, track 7, 0:00-0:53.

28:40-28:56 Mos Espa (part 1)
Omitted from the final film, this portion of the SONY CD track 7, running from 0:53-1:06, probably underscored Qui-Gon and Obi-Wan as they discussed plans and disturbances in the Force.

28:56-29:02 Mos Espa (part 2)
Here the music returns in the film, matching the SONY CD track 7, 1:06-1:14, a brief appearance before a segue into the next bit.

29:02-29:33 Mos Espa (part 3)
Edited out of the SONY album, but available, albeit with ambient Mos Espa sound effects on the TPM CD-ROM as file “sqespa1.imc”, this music underscores the conversation between Qui-Gon and Panaka as they argue about bringing Padme to Mos Espa.  A timpani roll functions as a segue back into the remaining section of this cue.

29:33-29:55 Mos Espa (part 4)
The SONY CD resumes here, on track 7, from 1:14 to 1:52, as our heroes journey into Mos Espa.

29:55-30:30 Mos Espa Source Music Unreleased
Exotic percussion is about all that can be heard of this cue in the finished film.  The TPM CD-ROM does contain some tracks of music and sound effects that sound like they could be some Espa source music, “espa04bar.imc” and “espa07bathhouse.imc”, though they bear little resemblance to the source music heard in the film.

31:07-32:15 "Are you an angel?" Unreleased
Anakin Skywalker is introduced, and his theme makes its first appearance in this unreleased cue.  After presenting this theme, the cue then segues into Jar Jar material, accentuating his comic antics with the pit droid.

32:15-32:17 "Hit the nose!"
One of a few cues available eclusively in the Episode 1 Insider’s Guide software CD-ROM, this music is the comic punchline to the above cue, and it’s even shorter in the film than it is on the CD-ROM.

32:17-33:51 Mos Espa Source Music Unreleased

34:28-35:41 Jar Jar and Sebulba
Heard in the Sony CD as part of track 4, this cue runs on disc from 3:50-5:07, the end of the track, and underscores the scene where Jar Jar gets in trouble with Sebulba and is bailed out by Anakin.

35:41-35:58 Obi-Wan and Panaka Unreleased
This cue is comprised of some unison low string writing and some sustained high string chords.  It functions as a link between the previous and next cues.

35:58-36:09  The Sandstorm (part 1)
This cue is featured in the SONY CD, track 4, running from 2:05-2:19, where an edit takes place.

36:09-36:19 The Sandstorm (part 2) Unreleased
These ten seconds where trimmed out of the SONY CD.  There is nothing with a particularly distinguishing quality in this brief passage.

36:19-37:07 The Sandstorm (part 3)
37:07-37:56 Meet See-Threepio
The SONY CD picks back up here, and the rest of these two cues are presented, from 2:19-3:50.

37:56-38:08 "Naked?!" Unreleased
This cue remains unreleased, and consists of some sustained brass chords and a timpani roll into a shot of a stormy Tatooine village.

38:08-38:24 Sio Bibble's Plea
38:24-38:44 CoruscantNOW AVAILABLE
38:44-39:12 "At last we shall have revenge…”
The bulk of these three cues, really one continuous cue in the film, can be heard in the TPM CD-ROM as file “sqairshafts.imc”.  The middle twenty seconds are now available in the "Jedi Power Battles" game for Sony Playstation.  These moments consist of a brassy fanfare that introduces us to the city-planet of Coruscant, heart of the Galactic Republic.

40:00-42:50 The Dinner Scene/Watto's Shop Unreleased
A signifigant amount of unreleased music comes from scenes on Tatooine, focusing on family-type material, and this cue is one such example.  There is warm string writing to underscore the kindness of young Anakin, and gentle woodwinds as well.  As the boy convinces everyone he can win the race and help them, a lovely “homestead”-esque theme is heard, before an uplifting statement of Anakin’s theme appears.  Finally, some string writing lends a bounce to Qui-Gon’s step as he marches to Watto’s the next day.  When Padme questions Qui-Gon’s plan, the music slows back down and tails out.

43:41-44:08 Dealing with Watto Unreleased
The first twenty seconds or so of this cue can be heard, under dialogue and other music, in the "One Will – Queen Amidala” Tone Poem.  The remaining 0:07 have yet to be released, and consist of a magical gliss up a bell tree before segueing into the next cue.

44:08-44:22 A Ship in a Desert
This cue is found on the SONY CD, track 11, from 1:37 to 1:52.  It is also tracked into the end of the Gungan battle, as all the droids are shut off from the explosion of the control ship.  In that appearance, the glockenspiel has been mixed out.

44:22-44:39 "…stuck here a long time…" Unreleased
Another small piece of unreleased music, this consists mainly of sustained string notes with woodwind  phrases played over them, all of a mysterious nature.  We then segue back into the CD recording.

44:39-47:35 Qui-Gon and Shmi/Kids at Play
Found on the SONY CD on track 11, from 1:52-4:57, the end of the track.

47:35-47:57 "It's working!"
A second cue found on the Episode 1 Insider's Guide CD-ROM, this cue is a moving little piece that underscores the firing up of the pod engines.  It has been referred to on the Internet as “Celtic sounding”, and can also be heard in the Qui-Gon Jinn Tone Poem.

47:57-48:58 Night time Unreleased
Lasting just over one minute, this unreleased cue is actually a continuation of the previous.  It features a pseudo-Arabian melody in the oboe before moving into some gentle music and a flute rendition of Anakin’s theme.  As Qui-Gon has Anakin’s blood analyzed, the music becomes darker and more mysterious, nicely leading into the next cue.

48:58-49:54 Darth Maul arrives on Tatooine
Whispered choral motifs, heard only in the film version, alert the audience that Darth Maul is nearby, and this music underscores his arrival to Tatooine.  Heard in severely edited form as the opening of track 5 on the SONY CD, the full-length version, minus the choral whispers,  can be heard in the TPM CD-ROM as “sqtense1.imc”.

49:54-50:53 Mos Espa Source Music Unreleased
About a minute of source music as Qui-Gon talks to Watto in the podrace hanger.  It fades out as the next cue begins.  Again, this cue seems to be mainly percussive.

50:53-51:59 Watto's Deal (part 1) 0:00-1:12
51:59-52:22 Watto's Deal (part 2) Unreleased  0:23
52:22-52:33 Watto's Deal (part 3) 1:12-1:23
This cue appears on the SONY CD, track 11, virtually complete, but there are about 23 seconds which appear in the film that are edited out of the soundtrack album.

52:33-52:46 The Probe Droid
ALT: Orig version
There are two versions of this cue.  The SONY CD contains the original version, which can be heard on track 11, 1:23-1:38.  However, in the film, the music written for Darth Maul’s arrival at Tatooine, “sqtense1.imc” on TPM CD-ROM, is used instead.

52:46-53:57 The Flag Parade
One of the highlights of the soundtrack (track 7 on the SONY CD, 1:52-4:04 (end of the track)) and included in an expanded form in John William’s symphonic suite drawn from the score, this cue is actually shorter in the film, having been edited down in length during the final mix.

53:57-55:09 Before the Podrace
Another wonderful cue, with a clever interpolation of Jabba the Hutt’s theme in the low brass, this cue is also shortened in the film.  Track 9 on the SONY CD, 0:00-1:12 is heard in the film.  However, when the contestants fire up their podracer engines, the music ducks out.  On CD, it continues until 1:35, the result being a little more than 20 seconds of music left out of the final film.

4:16-4:26 Anakin Versus Sebulba
The SONY CD, on track 9, starts at 1:35, with the suspenseful orchestra hits that coincide with Anakin’s pod malfunctions.  This continues until 1:54.

4:26-5:52 TRACK: Escape from Naboo
At this point, the film switches gears and uses tracked music from the “Escape From Naboo” and “The Heroics of Artoo-Detoo”, while the version on the CD appears to be music originally intended for this tracked scene.  However, the music on the CD is much shorter than the sequence in the film.  The omitted music can be heard on the CD from 1:54 to 2:27.

5:52-6:20 TRACK: Anakin Defeats Sebulba
This music is available on the EPISODE 1:RACER CD-ROM game, in the *.wav file titled "PodLoop1".  It is characteristic John Williams action music, full of brassy articulations and energetic percussion.
UPDATE Recently, www.starwars.com posted a quicktime movie about the sound in SW:E1:TPM and in it, they show what appears to be a dubbing session for the podrace.  Listen carefully, and you will hear what appears to be the music originally scored for that scene.  Guess what?  It's the "Anakin Defeats Sebulba" music as it appears on the SONY CD, track 9.  In other words, SONY CD track 9 is the music as John Williams originally wrote it for the podrace.   That means the music in the film was all tracked.  Which leaves the question:  "Where did this 28 seconds of music originally go in the film?"

6:34-6:41 Victory (part 1)
6:41-7:07 Victory (part 2) Unreleased
7:07-7:12 Victory (part 3)
Anakin wins the podrace, and Williams provides celebratory music, the bulk of which is unreleased, although a few moments can be heard on the TPM CD-ROM as the files “sqyay1.imc” and “sqyay2.imc”.  Neither file presents the entire cue, even when edited.  Believe it or not, for two cues that are so short, they were edited quite a bit by the makers of the CD-ROM.  (*Note – if you win the entire game, you are treated to a computer-graphic cut-scene of the victory parade on Naboo, much like the closing parade in the film.  Interestingly enough, the makers of the video game scored the scene with the full version of this cue, rather than the music used in the film, “Augie’s Municipal Band”.  However, there are quite a bit of sound effects and cheering obscuring the music.  This theme reminds me of "Heigh Ho" from Disney's Snow White and The Seven Dwarfs.)

7:12-7:38 "We owe you everything..." Unreleased
A variation on Anakin’s theme, presented in typical fashion in the woodwinds, closing with a lovely harp arpeggio.

7:35-8:20 Mos Espa Source Unreleased
More of the percussive source music, which plays as Qui-Gon and Watto talk in Watto’s stadium box-seat.

8:20-9:32 Back to Mos Espa Unreleased
The theme for Qui-Gon Jinn makes its first appearance here, presented in pseudo-classical style in the low strings with woodwind accents.  The theme continues until Qui-Gon and Anakin enter the hovel and show Shmi all the money they got for selling the pod.  At this point, we are presented with music much like the dinner scene, with a horn motif that is subtly recalled a few cues later.

9:32-10:03 "It's a hard life..."
This cue can be heard in the Episode 1 Insider’s Guide.  It is a gentle rendering of the Force theme and a variation of the “B” theme of the main title.  It closes with some spritely “kiddie” music, featuring John William’s characteristic use of a “celeste”-like synth.

10:03-10:20 Anakin and Shmi (part 1) Unreleased
The music turns sad and somber as Anakin realises that following his dream means he must leave his mother.

10:20-10:35 Anakin and Shmi (part 2) Unreleased
Heard under narration in the "One Love-Shmi Skywalker" Tone Poem, this cue features the horn motif introduced in "Back to Mos Espa", as well as a pretty melody played on an ethnic wooden flute.

10:35-12:30 Anakin and Shmi (part 3) Unreleased
The lovely flute melody continues while Shmi tells Anakin that she loves him.  As Qui-Gon assures Shmi he will look after Anakin, the music warms up, and continues as Anakin bids farewell to C-3PO, ending with a stirring musical gesture over 3PO’s distress at the possibility of being sold.  As Anakin leaves the home, he runs back to Shmi, and the music centers on the woodwinds, bittersweet and moving.

12:30-12:52 "I will come back..."
The TPM CD-ROM file “sqmaulintrocs.imc” contains music heard here, under minimal ambient sound effects.  The cue begins with the horn motif heard in “Back to Mos Espa” and “Anakin and Shmi (part 2)”, before english horn plays a sad melody.

12:52-13:11 "Don't look back..." Unreleased
Perhaps the most moving presentation of the Force Theme in “The Phantom Menace”, this cue can be heard under narration in the last portion of the "One Love-Shmi Skywalker" Tone Poem.  It is nineteen seconds long.

13:11-13:23 Darth Maul's Speeder Unreleased
Choral whispers return, as well as the snareless drum roll and high strings/woodwind clusters that characterize Darth Maul.

13:23-14:25 Duel in the Desert
TPM CD-ROM file “sqfightmaul1.imc” contains this cue, which begins with low brassy clusters before a grand orchestral drum cranks the music up a notch as Qui-Gon and Anakin run through the desert.  Maul arrives, swordplay ensures, and Qui-Gon’s theme is given a classy presentation complete with glockenspiel.  The main Star Wars theme even makes an appearance as the Queen’s ship lifts off.  The music changes color as Qui-Gon leaps to safety and Darth Maul watches our heroes escape from the desert world of Tatooine.

14:25-14:49 Anakin meets Obi-Wan (part 1) Unreleased
These twenty-four seconds are edited out of the track as it appears on the TPM CD-ROM, and consists of a clarinet somberly presenting Qui-Gon’s theme before the woodwind section plays with the Force theme as Anakin meets Obi-Wan Kenobi.

14:49-14:53 Anakin meets Obi-Wan (part 2)
The brassy flourish that closes this cue can be heard in the TPM CD-ROM as the end of “sqfightmaul1.imc”.

14:53-15:24 Sio Bibble and Nute Gunray
15:24-16:00 Padme views the transmission
These two cues are presented on track 13 of the SONY CD, from 0:00-1:07.

16:00-16:20 Padme and Anakin (part 1) Unreleased
This twenty seconds of music was edited out of the SONY CD.  Woodwind gestures dance around Anakin’s theme as Padme tells of the Queen’s troubles.

16:20-17:08 Padme and Anakin (part 2)
17:08-18:04 Arrival at Coruscant (part 1)
The SONY CD resumes here with Anakin’s theme through his conversation with Padme, then the brass fanfare and colorful string writing that signifies the arrival at Coruscant.  All can be heard on track 13 from 1:07-2:52.  A porion of this music is also heard on the SONY CD as the closing segment of track 1.

18:04-18:48 Arrival at Coruscant (part 2)
The TPM-CD-ROM file “sqbigcity.imc” contains music heard after the low string figure that closes SONY CD track 1, and is heard again at 2:52 on track 13. It continues through the meeting on the landing platform and into Palpatine’s quarters, ending as the Senator tells Amidala of the desperate situation in the Republic.

19:40-20:14 "That is something I cannot do..."
This cue, found as file “sqpalpatine.imc” with ambient sound effects on the TPM CD-ROM, is heard as the Queen tells Palpatine she will not let the corruption of the Senate compromise the well being of her people. *NOTE – the track on the game has looped the opening phrase so that it features a repeat not heard in the film.

20:14-21:52 The Jedi Council Unreleased
This is some cool, dark synth music that accompanies Qui-Gon’s description of the Sith warrior he fought on the desert world, continuing as he tells of the “vergence in the Force”.  The music lightens considerably at one point, and we are presented with Anakin’s theme,  voiced as usual primarily by woodwinds.  The cue concludes with a variation of the horn motif heard during the scenes where Anakin says goodbye to his mother.

21:52-22:40 Anakin and the Queen Unreleased
This unreleased cue is suspenseful and pensive, somewhat dark, though softening a bit as the Queen reassures Anakin. Then it darkens up and swells in orchestration as we travel to the Senate Chamber.

23:55-25:32 The Senate/Jedi Balcony Unreleased
Dark music is introduced as the Queen runs into a beauracratic roadblock in the Senate.  This dark music continues as Valorum is ousted from office.  In the next scene, Qui-Gon and Obi-Wan talk on the balcony at sunset, and the score is somewhat active for a scene of two people talking.  No signifigant themes, but rather, appropriate textural writing. [From a compositional point of view, I have been intrigued by this cue since I first saw a clip on TV, weeks before the film opened.  The score carries the drama of the Senate into Qui-Gon and Obi-Wan’s conversation quite a bit, creating about a five second overlap.  Interesting spotting there.  I wonder if the senate sequence was originally longer, and Lucas/Wannberg simply let the music run at it's original length, thus overlapping into the balcony scene...]

25:32-28:37 Anakin is Tested/The Queen's Decision Unreleased
Continuing arguably the longest chunk of unreleased music in the film, we now watch (and listen) as Anakin is tested before the Jedi council.  Mysterious and varied orchestrations of Anakin’s theme are heard, underscoring Anakin’s fear and longing for his mother.  The Force theme pops up when Yoda talks about fear and hate and suffering, then strings take over, brightening at first, then darkening considerably as Jar Jar and the Queen discuss the somber future of the residents of Naboo.  The tone lifts again as Palpatine enters, happy with his nomination as Supreme Chancellor.  Then it’s dark once more when Amidala voices her plan to return to Naboo.  The energy picks up as everyone marches out of the room.

28:37-32:13 The Chosen One/Midichlorians
This cue appears on the SONY CD in its entirety, without edits, on track 8.

32:13-32:39 Darth Sidious sends Maul to Naboo Unreleased
More of the Sidious theme.  I wouldn’t be surprised if this was a tracking of the cue “Darth Sidious” from the opening of the film, the orchestration is that similar.  UPDATE:  In fact, the same person who informed me that the Sidious material from the opening of the film remains unreleased informed me that the cue I have there ("sqeerie.imc") is in fact the score to this scene.  It is twenty-six seconds long.

32:39-34:43 Back to Naboo (part 1)
The heroes return to Naboo, and this cue underscores their journey.  Strong writing in the strings and brass accentuate the military underpinnings of the Queen and her entourage.  A strong brass fanfare signifies the landing on Naboo, and characteristic John Williams' orchestrations and harmonies support Qui-Gon Jinn and Obi-Wan Kenobi as they discuss the future and make amends for the past.  Finally, comical music appears as Jar Jar returns from his inspection of Otoh Gunga.  SONY CD track 6, 0:00-2:06.

34:43-35:00 Back to Naboo (part 2) Unreleased
Approximately seventeen seconds of textural music was edited out of the CD the track at this point.  In the film, the music underscores Jar Jar and Panaka as they discuss what has happened to the all the Gungans who deserted the underwater city.

35:00-35:33 Audience with Boss Nass (part 1)
35:33-35:56 Audience with Boss Nass (part 2)
35:56-37:18 Audience with Boss Nass (part 3)
This cue appears virtually as-is on the SONY CD, track 6, with the exception of the about twenty-three seconds of music which can be heard in the TPM CD-ROM in file “sqgarden.imc”, with ambient sound effects, and were edited out of the CD at 2:38.  At this point, the SONY CD continues to the end of the track, 4:07.

37:18-37:38 "An unexpected move..." Unreleased
Another twenty seconds of unreleased music.  Nothing too melodically distinctive, but rather, dark and textural.

37:38-38:12 Battle Plans (part 1)
Serving as the 'score' for one of the “Behind the Scenes” movies in the Episode 1 Insider’s Guide, this cue appears in the film as the Gungans announce Panaka’s return from Theed and Anakin runs to tell the Queen.  Meanwhile, Boss Nass promotes Jar Jar to the rank of Bombad General.  This cue reminds me of “For He’s A Jolly Good Fellow.”

38:12-39:39 Battle Plans (part 2) Unreleased
1:27 of unreleased music covering the dialogue-driven scene as Amidala outlines her plan for the retaking of Theed.  Once again, John Williams uses orchestral texture, rather than melody, to underscore the scene.  Effective writing, if perhaps unremarkable.  The cue ends with a clarinet phrase reminiscent of  “Return of the Jedi”.

39:39-40:05 "Wipe them out..."NOW AVAILABLE
Twenty-six seconds of dark brass texture before a small flourish segues directly into the next cue.  Available in the "Jedi Power Battles" game for Sony Playstation.

From this point on, until the cue “The Energy Shields”, the score becomes heavily edited and fragmented.  It is my opinion that virtually all of the music in these scenes is cut into the film differently than John Williams originally conceived it.  I attribute this to heavy re-editing of the picture late in the post-production process, after the music had already been recorded.  Ken Wannberg alludes to this in a recent interview, as does John Williams in MIX Magazine.

40:05-40:36 The Gungan March
This cue is found on the SONY CD, track 14, 0:00-0:31.  The horns being blown ny the Gungan warriors do not appear on the soundtrack album, and it is my guess that they were added by Ben Burtt and his sound crew and not part of the music scoring session by John Williams.

40:36-40:51 TRACK:Message from Palpatine
As the Gungans power up their shield generator, the score reverts to an earlier cue, which can be heard on the SONY CD, track 13, from 4:08-4:23.  I presume this is not how John Williams intended to score this scene.

41:16-41:35 Naboo Courtyard Unreleased
About twenty seconds of “sneaking-around” music.

41:36-41:55 The Fighting BeginsNOW AVAILABLE
The “Duel of the Fates” motif makes its first appearance in the score is this cue, a short (0:19) burst of energy as the first moments of battle take place.  The opening flourish sounds like the same one heard at the very beginning of “Omitted Action Music” (“sqfight5.imc” - an omitted cue).

41:55-42:01 TRACK:  "This is too close..."
This short segment is six seconds long and is tracked in from the cue “Jedi Fight”, found on the TPM CD-ROM as “sqdroidfightloop.imc”.

42:01-42:17 Entering the Hangar - Anakin Hides
42:17-42:52 The Ships Lift Off
These two cues are pulled from SONY CD track 12, in opposite order than they appear in the film.  The first runs from 0:36-0:54, the second from 0:00-0:36.

42:52-43:00 Back in the Hangar
Eight seconds of action music, punctuated by xylophone.  It can be heard in the file "psycheloop" on the RACER cd-rom.

43:00-43:04 Engaging the Federation Battleship (part 1)
43:04-43:08 Engaging the Federation Battleship (part 2)
43:08-43:16 Engaging the Federation Battleship (part 3)
These three cues are really one, edited version of track 5 from the SONY CD, using 0:21-0:25, 2:16-2:20, and 2:22-2:30.

44:04-44:47 Activating the Battle Droids
From the SONY CD, track 14, 0:31-1:05.

44:47-45:13 "Stay in that cockpit..."
From the SONY CD, track 12, 1:10-1:43.

45:13-45:25 Darth Maul
From the SONY CD, track 15, 0:00-0:13.

45:25-45:59 Drawing Swords (part 1)
45:29-45:38 Drawing Swords (part 2)
Edits of material from the SONY CD, track 2, 0:39-0:43 and 2:17-2:25.  *NOTE – this recording of “Duel of the Fates” was originally intended to be used solely in the end credits and as a concert arrangement, but according to a recent interview with Ken Wannberg, George Lucas liked it so much he began tracking it in all the sword fighting scenes.

45:38-45:49 Drawing Swords (part 3)
This cue is unreleased, but it matches track 2 from 2:55 to 3:07.  It is essentially the same music, simply instrumental, without the choir.

45:49-45:59 Drawing Swords (part 4)
More material from SONY CD track 2, 3:07-3:22.

45:59-46:46 Anakin Takes Off
From SONY CD, track 12, 1:57-2:40

46:46-47:16 The Jedi Versus Sith (part 1)
47:16-47:26 The Jedi Versus Sith (part 2)
47:26-47:31 Gunfight in the Hallway (part 1)
47:31-47:44 Gunfight in the Hallway (part 2)
Material pulled from SONY CD track 2.  First is 2:37-3:07, which underscores the Jedi duel.  Next is 3:07-3:22, which continues this scene.  Then we move to the gunfight in the hallway, and 2:17-2:19, which is looped to last 5 or so seconds.  Finally, we hear 2:19-2:37, edited from roughly eighteen seconds to roughly thirteen.

47:44-49:40 The Battles Continue
A fairly straight, uncut presentation of SONY CD track 5, 0:26-2:31.

49:40-49:48 Ascension Guns (part 1)
49:48-49:54 Ascension Guns (part 2)
49:54-50:00 Ascension Guns (part 3)
50:00-50:27 Dueling on the Catwalks (part 1)
50:27-50:51 Dueling on the Catwalks (part 2)
More material from SONY CD, track 2.  First is 0:58-1:02, which is looped to play twice.  Next is 1:15-1:21, then 1:58-2:04, which underscore the actions of the Queen as she tries to retake the palace.  Following that is 3:07-3:35, as we return to the lightsaber duel, and finally, 3:43-4:09, the end of the cue, which perfectly punctuates the imposed interlude in the sword fight.

51:05-51:18 The Energy Shields Unreleased
As soon as the energy shields activate, the pulsing rhythms of “Duel of the Fates” reach their cadence and the score changes gears.  We are now presented with thirteen seconds of high strings with flourishes in the piano and flute.  Suitably unsettling.

51:18-52:50 TRACK:  The Gungans Retreat
Big brass chords and more classic John Williams action “ballet” as he underscores the retreat of the Gungans after their shield is destroyed.   UPDATE The music that scores this scene in the movie was originally written for the podrace sequence as Anakin repairs his engine and defeats Sebulba.  That explains a little controversy as to why Anakin's theme is heard as Queen Amidala is captured by the Nemoidians at the end of this cue:  it was originally supposed to score Anakin's defeat of Sebulba, hence his theme.  This cue is found on the SONY CD on track 9, from 2:27-4:13, the end of the track.

52:50-53:31 Anakin Crashes on the Federation Ship
This cue can be found on the TPM CD-ROM as file “sqgripping1.imc”.  Its finale resembles a section of the concert arrangement of "Duel of the Fates” and it ends with an homage to serials of old, with tremolo strings heightening the tension.

53:31-55:46 Qui-Gon's Noble End
At last a segment of this cue which actually jives with the title it was given on the SONY CD.  Track 15, from 1:29-3:47 (the end of the track) is heard in the film as Maul paces, waiting for the energy shields to deactivate, before dueling with Qui-Gon.  After Jinn is defeated in battle, we see the Gungan army being subjugated by the Battledroids.  The cue ends as Queen Amidala is captured by the Nemoidians, then fights to regain her freedom.  We return to the reactor room as Obi-Wan prepares to face Darth Maul, a scene left virtually music-free.

(54:01-54:18) (manic flutes and piccolo overdub)
This cue appears on the TPM CD-ROM as the opening moments of “sqgripping1.imc”, but is heard in the film superimposed over the previous cue as Darth Maul duels with Qui-Gon Jinn moments before striking him with his lightsaber.  It is very simply some frenetic piccolo and flute jabs played in a manic style.  I believe it was intended to go here, but was tacked onto the beginning of “sqgripping1.imc” by the game makers at LucasArts, superimposed over the percussive intro for use in the CD-ROM.

56:27-57:54 Anakin Destroys the Federation Ship
A nice piece of action music that starts in 7/4 time, this cue underscores Anakin as he blows up the reactor and destroys the droid control ship.  It can be heard in the TPM CD-ROM as file “sqreactor.imc”.  It features a presentation of the “Duel of the Fates” theme and the Force theme.

57:54-58:10 TRACK:A Ship in the Desert (remixed)
After Anakin destroys the Federation Droid control ship, the score is tracked with a cue from Tatooine earlier in the film, “A Ship in the Desert”, which is remixed to eliminate the glockenspiel and more brightly colored musical elements.

58:14-58:29 Obi-Wan Comes of Age Unreleased
This cue can be heard under narration in the fifteen-second “Amidala” TV commercial, and is another orchestration of the Force Theme as Obi-Wan culminates his apprenticeship to Qui-Gon Jinn and masters the Force to defeat Darth Maul.

58:29-59:36 The Death of Darth Maul
The Death of Qui-Gon Jinn
These two cues, most likely recorded as one long cue beginning with “Obi-Wan Comes of Age” and ending with the final notes of this cue, are found as the files “sqmauldeathloop.imc” and “sqquigondeath.imc” on the TPM CD-ROM.  The former cue has some low-end/rumble sound effects on it.

59:36-1:02:31 Palpatine Arrives on Naboo/
Yoda and Obi-Wan Kenobi/
Funeral for Qui-Gon Jinn
This cue appears without edits on the SONY CD as track 16.  Note that the opening strains are a reprise of the “homestead” theme from the dinner scene with Anakin, Shmi, Qui-Gon, Jar Jar and Padme.

1:02:31-3:51 Naboo Parade Unreleased
1:03:51-end End Credits
This cue is presented on the SONY CD as track 17.  The Parade portion of the cue differs from the film version, I suspect, because it was mixed once by Shawn Murphy in a separate session for the CD, and then again by the re-recording mixers in the dubbing session for the film (much like the “Ewok Celebration” and “Lapti Nek” from the original release of RETURN OF THE JEDI).  The end credits appear as-is in the film, although the closing moments of “Anakin’s Theme” feature the sound of Darth Vader’s mechanical breathing for added foreboding.  With track 16 and the majority of track 17,  THE PHANTOM MENACE ends fairly darkly for what is mostly a bright kid’s film.  It is certainly a departure from the brassy fanfares that conclude episodes 4, 5 and 6.  Bodes well for parts 2 and 3, supposedly the darkest of the six films.