Marvel 2099 "One Nation Under Doom" saga to the beginnings of the Ghostworks 2099 UnderGround

Doom 2099UG #1-#3 (Happen directly after Doom
2099 #38)
Spider-Man 2099UG #1
Morbius 2099UG #0-#3
Punisher 2099UG #0-#8 (Takes places after the
final issue of Punisher 2099 series)
Fantastic Four 2099UG #1-#4 (mini-series, takes place
after FF 2099 #4)
Iron Man 2099UG #1-#3 (Volume 1)
Ghost Rider 2099UG #1
X-Men 2099UG "Gravity"-#37 (series takes place after X-men 2099 #31)
Thor 2099UG #1-#2
Hulk 2099UG #0-#3

Beginnings of the Ghostworks 2099 Underground to the "Fall of Alchemax"

Spiderman 2099UG #2-#7
Morbius 2099UG #4-#11
Ghost Rider 2099UG #2-#10
Punisher 2099UG #9-#17
Thor 2099UG #3-#10
Doom 2099UG #4-#15
Salem 2099UG #1-#7
Iron Man 2099UG #1-#4 (Volume 2)
Archangel 2099UG #1-#11
X-Men 2099UG #38-#50
Tensen 2099UG #1-#14
Hulk 2099UG #4-#5
Captain America 2099UG - The Legacy Collection
Black Panther 2099UG #1-#4

"Fall of Alchemax" to the "Coming of Galactus" & 2099 New Year's Eve

Theater of Pain 2099UG
#1-#4
Doom 2099UG #16-18
Captain America 2099UG - The Deadpool #1-#4
Spider-Man 2099UG #8-#9
Salem 2099UG #8
Alpha Flight 2099UG #1-#5
The Coming of Galactus 2099UG #1-#4

2099 New Year's Eve and onward...

2099UG: Tomorrow Anew

2099UG Tales #1-#2
X-Men 2099UG #1 (Volume 2) and onward
Iron Man 2099UG #1 (Volume 3) and onward
Null 2099UG
Daredevil 2099UG
Continuity Guide
This nifty little Continuity Guide here will help you in your trek through the world of 2099.  Right now you are seeing the rough draft of a much larger project that will include: appearance guides, crossover events, and loads more information!  But this should help the newbies with where issues fall on a timeline in relation with each other.