Engineering Terms & Devices
With special thanks to Marcel van Wijk for some of the info.  Other data from ST: Omnipedia, Encyclopedia, and Concordance.
Partial list only.  More will be added as I get time, and as writers dream up more :-)

A
NAME
DESCRIPTION REFERANCE
ACB Abbreviation for Annular Confinement Beam
Ablative Armor A strong metallic alloy that protects a starship hull from damage due to heat and beam weapons (phasers, etc...). Voy: Message in a Bottle - The USS Prometheus had Ablative Armor.
DS9: Most - The USS Defiant is equipped with Ablative Armor.
Aceton Assimilator Weapon used by the ancient Menthars in their war with the Promellians a thousand years ago. Aceton assimilators could drain power from distant sources (such as a hostile ship), then turning that energy into deadly radiation to kill the ship's crew.  No apparent link with the chemical substance aceton. TNG: Booby Trap - Hundreds of thousands of these devices were placed in an asteroid field near Orelious IX, trapping the Promellian cruiser 1,000 years ago. While still active now, they trapped the Enterprise-D in 2366.
Adaptive Interface Link Computer connection used to exchange information between two computer systems of different alien origin. DS9: The Forsaken - An adaptive interface link was used to download information from an alien space probe of unknown origin to Deep Space Nine's computers.
Alternate Reality Parallel universe, which is a copy of our universe, but with a different timeline. Voy: Non-Sequitor - Harry Kim encountered an alternate realite in which he remained on Earth.
Alternative Warp A FTL drive that exists of a negative magnetic corridor in which universes come together. The corridor is not supposed to breach. TOS: The Alternative Factor
Ampheon Term used for a dead star in an antimatter universe. TOS: The Counter-Clock Incident
Android A mechanical life form. Can appear, react, think, learn and acts like a human.  Designs may vary. TOS: What are Little Girls Made Of - Androids were made by technology left by an ancient race.
TOS: I, Mudd - An entire race of Androids.
TOS: Requiem for Methusela - An Android was created to be a companion for Flint.
TNG: ALL - LCDR Data is an Android
TNG: Various - Lore, the twin 'brother' to LCDR Data.
TNG: Offspring - LCDR Data creates a "daughter".
Voyager: Prototype - Automated units.
Annular Confinement Beam (ACB) Aiding beam of a transporter.  The beam serves two purposes: The first is to maintain a 'lock' on the subject, so the transporter knows what to beam out, and what to leave behind. The second purpose is to do the actual transporting, whilst keeping the subject in one piece subjectively. ALL
Antigrav Portable device used aboard Federation starships for handling cargo and other items too large for a single crew member to carry. The mechanism after it is called a graviton inverter circuit. TNG: Hollow Pursuits
Antigrav Thrusters Used on ships able to land on planetary surfaces, thrusters utilize antigravity to raise a ship from a planetary surface. Voyager: Demon
Voyager: The 37's
Antimatter Form of matter, existing of the same particles as normal matter, but with inverse properties (like electrical charge and direction of rotation spin).  If matter and antimatter are brought together, the mass energy of the matter and antimatter particles will be converted to pure electromagnetic energy.  Because of the giant amounts of energy that are released at this reactions, matter/antimatter-reactors are used as warp core. ALL
Antitime Time and antitime are like matter and antimatter. When time and antitime collide, a breach in space-time is formed.  Antitime is not forbidden by relativity, it even seems to be supported by general relativity (according to 'The Physics of Star Trek' by Lawrence Krauss).  Stephen Hawking played a while with the idea of antitime in a contracting universe, but the idea was considered as wrong.  However, it's possible that in the center of a black hole antitime is running.  The antitime phenomenon in the Devron system caused three alternative realities - one in 2364, one in 2370 and one in 2395. TNG: All good Things - antitime was mentioned as 'a occurence of multi-phasic temporal convergence'. The phenomenon was actually caused by the Q Continuum, who devised this test as a test of mankind, to learn if humanity could stretch its mind to comprehend other levels of existence.
Anyons Particles produced by the interaction between phased matter and normal matter.  In real life, an anyon isn't a real particle, it's a theoretical construction formed by confining a fermion (matter particle), and possibly boson (energy-carrying particle), to a two-dimensional region. TNG: The Next Phase
Atavachron Temporal portal developed on the planet Sarpeidon to travel through time.  The atavachron alters a time traveler's cellular structure, making it possible to survive in earlier environments, but also making it impossible to return to the present without reversing the alteration. TOS: All Our Yesterdays - the people of Sarpeidon used the atavachron to escape into the past when their sun, Beta Niobe, went nova in 2269

B
NAME DESCRIPTION REFERANCE
Baryon Sweep All matter we see - including ourselves is composed of Baryons.  A 'Baryon Sweep' is a procedure where high-frequency plasma is used to remove baryon particles from a starship.  During extended periods of warp flight, baryon particles build up on the starship, requiring periodical decontamination.  The procedure is deadly to a starship's crew, requiring complete evacuation of a starship before the procedure is executed.  It is logical that the baryon sweep is deadly to humans, because it removes all baryon particles it encounters - so all the protons and neutrons in the atoms of humans!  In reality, a baryon sweep would completely dematerialize a starship, leaving only a cloud of electrons behind.  Weird, because while Baryons are deadly to humanoids, without them we are unable to live! TNG: Starship Mine - The Enterprise undergoes a Baryon Sweep.
TNG: Suspicions - Baryon particles were partially responsible for Jo'Bril's death
Berthold Radiation Artificially generated by aliens. Unknown purpose. TNG: Deja Q - A method employed by the aliens to scan the enterprise D when the aliens were looking for Q.
Berthold Rays Naturally occuring. Nature unknown. Harmful or fatal to humans. TOS: This Side of Paradise - The emotion-affecting spores granted immunity to Berthold rays, allowing a colony to survive.
Bilitrium Naturally occuring. A rare crystalline element which can be an incredible source of energy if hooked up to an anti-matter converter. DS9: Past Prologue - Tahna Los had purchased a cylinder of bilitrium from the Duras Sisters in an effort to destroy the wormhole.
Biochips Cybernetic implants surgically imbeded into bodies of the Borg.  They serve to enhance their physical abilities and synthesize any organic molecules needed by their biological tissues. The Borg are dependent on the implants, and would die if the biochips are removed. TNG: I, Borg
Biofilter Part of a transporter.  Used to filter out any harmful substances and/or life forms (like bacterial and viral agents).  The filter looks for elements of the pattern which aren't found in normal beings/equipment, or those of known viruses and bacteria.  It can simply erase those parts of the pattern, and those parts of the matter stream won't beam back in.
Biomatter Other name for organic material.
Bioship Spaceship made of biomatter.  In some cases the ship is "living".  Species 8472, and the Breen travel with bioships.  The bioships of Species 8472 are made of the same material as the aliens themselves, and are practically invunerable. TNG: Tin Man
Voyager: Scorpion I, II
Voyager: Prey
Black Hole An imploded star.  It's gravity is so strong, that even light is not able to escape from it.  The 'event horizon' is a geometric border of a black hole; inside the event horizon, the escape velocity is greater than the speed of light.  Black holes are the power sources of quasars, and can create wormholes, X-rays and gamma-radiation.  A subspace rupture is a phenomenon related to black holes. Voyager: Parallax
Boridium Artificially generated by crew. Used as a power generator or convertor in compact machines and devices. TNG: The Quality of Life - The Exocomps are equipped with boridium power generators.  Dr. Farillon attempts to destroy some of these Exocomps by overloading these generators.
DS9: Babel - The Aphasia-inducing device has a di-boridium core which hints at possible Cardassian manufacture, but was actually created by the Bajoran Underground during the Cardassian occupation of Bajor.

C
NAME DESCRIPTION REFERANCE
"C" (AKA Cochranes) Symbol that represents "Cochranes" - Named after Zephrem Cochrane, it measures the units of subspace distortion required for warp drives.  1 cochrane is the distortion required to propel a ship at lightspeed (warp 1).  Thus, to travel at warp 2 (10x lightspeed), a distortion of 10 cochranes is required. Voyager - The Gift - Cochranes are also used to refer to intensity of the Matter/Antimatter reaction.
Carbon Neutronium Artificially generated by aliens. TNG: Relics - The shell of the Dyson sphere was composed of it. A phaser blast was ruled out as an option to get out of the sphere because it would be ineffective.
Cast Rodinium Naturally occuring. The hardest substance known to Federation science. TOS: Balance of Terror - The outer protective layers of Federation outposts along the Romulan neutral zone are composed of this material. However, even with an outpost buried miles underground, it provided insufficient defense against the Romulan energy weapon. A piece of the destroyed shield was crushed by Spock.
Chroniton Particles, that are in a state of temporal flux (out of phase with the space-time continuum).  Chronitons have been used to create a temporal vortex for time travel, and are also involved with cloaking devices.  Torpedoes charged with Chronitons were also used by the Delta Quadrant race called the Krenim (chroniton torpedo). DS9: Past Tense - Used to travel back to 21st-century Earth.
TNG: The Next Phase - Chroniton particles from a malfunctioning cloaking device cause Geordi and Ro to be phased so they can pass through walls (not floors).
DS9: Visionary - Sent O'Brien back and forth in time whenever a cloaked warbird came near DS9.
Voyager: Before and After - When Kes was irradiated with chroniton particles from the Krenim and later subjected to a biotemporal field, she began to shift backwards in time.
Voyager: The Year of Hell - The ship passes through a region of constant border changes due to a temporal ship.
Chronometric Particle Artificially generated by aliens. Involved in time travel.  See Chroniton (above). Movie: First Contact - The Borg used them to travel back in time. The Enterprise-E used them to travel forward in time.
DS9: Trials and Tribble-ations - O'Brien reads chronometric particles around the Defiant just before it is pulled back in time by the Orb.
Cloaking Devices Device which makes a ships, bases -and even planets invisible to the naked eye and sensors.  The Aldeans, Romulans, Klingons, Voth and the Breen also use it.  There are multiple different types of cloaking devices.  One of the most common types project an energy screen formed by generator coils which cause particles and radiation to bend around the ship - thus making it undetectable.  However, cloaking by this type has a potential manner of detection - particles must travel a greater distance to go 'around' the cloak, and therefore an observer can detect photons affected by the cloaking field when they arrive later than non-affected photons.  To mask the energy emissions from the ship itself, the ships systems are powered by 'nullifier cores', which dissipate the energy that is used.  The Treaty of Organia forbids the Federation from using cloaking devices. TOS: Balance of Terror - A prototype Romulan ship attacks border outposts.
TOS: The Enterprise Incident - Kirk steals a Romulan Cloaking device.
TOS: The Deadly Years - The Enterprise is attacked by Romulan ships.
TNG: The Pegasus - A secret Star Fleet vessel with a prototype cloading device is discovered.
TNG: Unification I, II - A cloaked Klingon ship transports Picard and Data to Romulus.
TNG: When the Bough Breaks - Aldea is hidden by a planetary cloaking device.
TNG: Redemption II - A Tachyon grid is used to detect cloaked Romulan ships.
TNG: The Next Phase - Geordi and Ro are cloaked by prototype Romulan device. 
Voyager: Distant Origin - The Voth use cloaking devices.
DS9: Many - The USS Defiant is equipped with a borrowed Romulan Cloaking Device.
Movie: The Search For Spock - Klingon ship must decloak before firing.
Movie: The Voyage Home - Cloaking device is used to hide the ship while on Earth in the past.
Movie: The Undiscovered Country - Klingon ship capable of firing while cloaked.
Movie: Generations - A Rogue Klingon ship disables the Enterprise-D. 
Coaxial Warp A form of warp travel that works by locally folding space.  The core of the coaxial warp drive manipulates the geometry of incoming particles, which bends space. The field of bended space is called coaxial space.  Starfleet engineers consider this warp drive as hypothetical.  Coaxial warp is much faster than conventional warp, but it's unstable because flows of instable particles entering the core destabilize the coaxial field. Voyager: Vis a Vis - Paris proposes using Coaxial Warp.
Comlink Short for Communication link.  Normally done by hand-held communicators and combadges using subspace radio. ALL
Containment Field A special forcefield used to isolate dangerous materials.  Containment fields are used in antimatter storage pods to protect a ship against contact with the extremely volatile antimatter.  The same principle is applied to fields used for quarantine isolation and for containment of dangerous biological specimens. ALL refer in various episodes

TNG: Relics - The containment fields used in the warp drive on the old Enterprise needed to be phase locked within three percent in order to avoid instability, but by the time of the Enterprise-D, multi-phase containment fields were able to operate considerably above that value

Continuum Drag Theorical force, from which is said that it stops ships from accelerating while they at warp.  Continuum drag is comparable to air drag, but it's not air that influents movement, but the space-time continuum.  However, there's no need for a force like that to explain why sustaining a warp field needs a constant influx of energy.  This might be better explained by the fact that warp drive is non-newtonian, and is thus not explainable with Newton's laws.
Corbomite A fictional substance which supposedly reflects weapon fire back at the attacker. TOS: The Corbomite Maneuver - Kirk tells the First Federation captain that the Enterprise is equipped with corbomite, a bluff that prevents the alien from firing his weapons.
TOS: The Deadly Years - Kirk uses the same ploy to escape romulans!!
Corodum Artificially generated by crew. Used in thruster packs. TNG: Disaster - Geordi and Beverly had to get rid of the containers of corodum, because the plasma fire was overheating them. They opened the cargo bay doors, and released the containers into space.
Cosmic String Naturally occuring. A string of particles with gravitational forces that are the strength of a black hole. TNG: The Loss - A flurry of energy based entities surrounding the Enterprise D were headed for it, dragging the ship toward certain destruction. These creatures disabled counselor Troi's empathic powers for a time. The cosmic string was home to them.
Cryostasis State of low biological activity in a human body.  Cryostasis is achieved by preserving bodies in a cooling chamber. TNG: Tapestry - A Stasis unit is used to keep injured stable until medical attention can be given.
Voyager: The 37s - Humans survived 434 years in stasis chambers.

D
NAME DESCRIPTION REFERANCE
Dark Matter Naturally occuring. Causes phase shifts in normal matter. TNG: In Theory - Opened the wall for Spot to escape, wrecked the conference room, and dematerialized part of the floor, causing the death of a crewmember who was standing on the "hole."
De Broglie Waves Naturally occurring in real life -- in modern physics, a representation of ordinary matter as waves rather than particles. In Star Trek, artificially generated by aliens; a side effect of cloaking devices. TOS: Balance of Terror - In James Blish's novel adaptation, the crew tracked the Romulan Warbird by sensing these waves. (In the aired episode, Spock used "motion sensors" to track the ship.
Dechyon Artificially generated by crew. In real life, dechyons are the class of particles that travel below the speed of light (i.e., the opposite of tachyons.) Voyager: Parallax - Used to open a fissure in an event horizon (no, that concept doesn't make any sense to me either.)
TNG: Cause and Effect - The crew detected these particles as remenants of each "causality loop" and Data used them to send a message into the next loop, which allowed them to break this most vicious cycle.
Delta Rays Naturally occuring. Type of radiation produced by older engines; exists in real life. Delta-rays refer to moderate energy electrons which have been kicked off a nucleus by the passage of a nearby high energy charged particle. TOS: The Meangerie part I - Was emitted from a broken piece of an old class-J starship. Christopher Pike, former captain of starship Enterprise was overexposed in that accident leaving him in a "wheelchair."
DS9: Visionary - O'Brien absorbed a heavy dose of delta radiation, which allowed the tetryon emissions from the Romulan warbird to shift him through time.
Deuterium Naturally occuring. Isotope of hydrogen, having twice the mass of ordinary hydrogen, also called heavy hydrogen. TNG: Phantasms - Used to power the warp core. Deuterium and antideuterium are combined to provide energy.
Diburinium Origin unknown. A metallic substance. TOS: By Any Other Name - The substance used by the Kelvin to imprison Captain Kirk and company in the cave was described by Spock as "similar to diburinium, but much denser."
Diburnium-osmium Alloy Artificially generated by aliens. A substance highly resistant to energy and radiation. TOS: That Which Survives - An artificial planet was made of this substance. The Kelandans were the race responsible.
Dicosilium Origin unknown. Optic material used to build lenses and mirrors. TNG: A Matter of Perspective - Used to build Krieger wave generator.
Dilithium Naturally occuring. Focuses energy into highly concentrated form. Necessary for the operation of warp drives, and a vital part of a starship's power system. TOS: most - Cracked, running out, etc.
TNG: Relics - La Forge states to an out-of-time Mr. Scott that they recomposite the dilithium inside the reaction chamber. Only after Mr. Scott erroneously states that dilithium crystals are going to fracture.
Displacement Wave Artificially generated by aliens. Moves objects at high warp speed. Voyager: The Caretaker - Used by caretaker to bring ship to Delta Quadrant.
Dolamide Origin unknown. Used in power generators, reactors, and short-range transporters. If pure enough, it can be made into weapons. DS9: Dramatis Personae - Kira refuses a Valerian transport carrying dolamide to dock with the station under the suspicion that they are trading with the Cardassians.
Duranium Artificially generated by crew. A hard metal alloy.  Often used for ship's hulls. DS9: The Emissary - Duranium shadows were used to create an illusion of photon torpedo launchers on DS9. This effect is also known as "Quaker Guns" in the DS9 novel _The Way of the Warrior_.
DS9: Captive Pursuit - Used in construction of access tunnels on DS9; impervious to normal sensors.
TNG: Hollow Pursuits - O'Brien tested the transporter with a container made of pure duranium. The container rematerialized as molten goo.
Dynamic mode stabilizer A tool used to analize computer systems, and scan for anomalies. Most useful on isolinear, and bio-neural gel pack circuits. 3x19 cm

E
NAME
DESCRIPTION REFERANCE
Electro-Plasma Regulator This is used for the handling of EPS power relays, and the maintenance of the power conduits. Its dimensions are 5x36cm

F
NAME
DESCRIPTION REFERANCE
Fistrium Naturally occuring. Refractory metal found in caves of Melona IV. TNG: Silicon Avatar - Data thought the prescence of fistrium and kelbonite prevented the Crystalline Entity from scanning the caves.
Flow Distributor Used to redirect the power flow out of a relay from a damaged conduit/peripheral equipment (Replicators, etc). It can be used to adjust for the flow ratio of a power conduit/EPS flow regulator, or to realign the induction coils.
Fortanium Naturally occuring. TNG: Masks - Used in the composition of the informational archive at the comet's core.

G
NAME
DESCRIPTION REFERANCE
Genesis Wave Artificially generated by crew. An energy wave that has the effect of rapidly terraforming planets and nebular matter. Movie: The Wrath of Khan; The Search for Spock - The Genesis Device, invented by Carol and David Marcus, was sought by Khan Singh as a weapon to be used to destroy Admiral Kirk and the Enterprise NCC 1701. Ultimately, the device was activated, destroying the USS Reliant, killing Khan, and creating the Genesis Planet from matter in the Mutara Nebula. Because of the unusual properties of the planet, the body of Spock was brought back to life after he'd been killed saving the Enterprise.
Graviton Artificially generated by crew. Generated by Voyager. (A real particle according to modern physics.) Voyager: The Caretaker - To try and get out of the Caretaker's beam.
TNG: The Best of Both Worlds - A "heavy graviton beam" was considered and rejected as a weapon against the Borg.
TNG: Silicon Avatar - Used by Enterprise crew to communicate with the crytalline entity. Used by vengeful doctor to destroy the entity.
TNG: Hero Worship - Graviton waves destroyed the Veco when it was surveying a region of space.  Reacted with all power output by ships and magnified it.
TNG: The Nth Degree - Barclay used a graviton field to alter subspace to take the ship into Cytherian space.

H
NAME
DESCRIPTION REFERANCE
Hyperon Naturally occuring. Hyperons are a class of real particles whose name dates back to the days before quark structure was well known. Leptons (electrons, muons, tau and their associated neutrinos) are "light", Mesons are "medium", and baryons are heavy. When more massive short-lived particles heavier than the proton were produced, they were called hyperons. Some examples are the sigma lambda and cascade. After quark structure was understood, they first three names were kept, but the meaning was changed. Leptons are the same list as originally, but are understood to be fundamental particles with no quark structure. Mesons are quark-anitquark pairs. Baryons are triplets of quarks. The term hyperon is still used, but not so frequently. TNG: The Ensigns of Command - Obstacle preventing the use of transporters in the evacuation of a planet ceded to the Sheliak.
Hyper Spanner A tool used in the calibration of plasma injectors.

I
NAME
DESCRIPTION REFERANCE
Ilium 629 Naturally occuring. A by-product of the geological decay of dilithium. TNG: Pen Pals - Traces of ilium 629 were found on the planet Drema IV, leading to the discovery of unusual dilithium deposits in the planet's mantle. The dilithium transformed the planet's geological heat into mechanical stress, resulting in significant tectonic instabilities that nearly destroyed the planet. The geological instabilities were neutralized by the use of resonator probes launched from orbit.
Iogenic Particles Artificially generated by crew. Has characteristic 'magnetic flux density'. TNG: Power Play - Used to create a containment field for the 'spirits' of alien escapees of a penal colony when they attempted to possess the crew.
Ion Naturally occuring. An atom or group of atoms that carries a positive or negative electric charge. TOS: Spock's Brain - Used to propel the space ship that carried descendants of an advanced civilization who boarded the Enterprise and stole Spock's brain. Scotty marveled at its design at first sight, saying that "they could teach us a thing or two."
Ionic Pulse Artificially generated by crew. Presumably, a bunch of charged atoms. Movie: Generations - An ionic pulse generated by the navigational deflector was used to trigger the cloaking device of L'ursa and B'etor's ship so their shields would drop and the Enterprise could destroy them.
Isochronious Asymmetric Compensator Used for transporters. Has a variety of uses from realigning the phase transition coils, to adjusting the flow feed of the Doppler compensators.
Isolinear Enhancer Similar purpose to the Inducer, except it offers a phase regulator for those pesky ODN problems, requiring isolinear i-node probing. 25 cm long.
Isolinear Inducer This tool is used in a variety of tasks from replacing a damaged circuit to diagnosing anomalies in a bio-gel pack. It's shaped like a very crude looking broom handle, with a nice comfy easy grip ;-) It's about 25 cm long
Isolinear Phase Inverter This tool is used to probe Isolinear circuits for common problems. At current, it can be used as a diagnostic tool, or just something to pry the lid off a can of peanuts. The tool has a rather large, white light emitting diode at the tip of it. It's about 48 cm long, and very thick.

J
NAME
DESCRIPTION REFERANCE
Jakmanite Naturally occuring. Like invidium, jakmanite cannot be detected by internal sensors. Exists in oxygen environment, and like invidium, can alter advanced structures like glass. TNG: Hollow Pursuits - Duffy ruled jakmanite out as a possible cause of the problems experienced by the Enterprise crew.

K
NAME
DESCRIPTION REFERANCE
Kedion Naturally occuring. Resets positronic matrices. TNG: Descent, Part 2 - Used by Commander La Forge and Captain Picard to reboot Data's ethical program after Lore disabled it.
Kelbonite Naturally occuring. Refractory metal found in caves of Melona IV. TNG: Silicon Avatar - Data thought the prescence of kelbonite and fistrium prevented the Crystilline Entity from scanning caves.
Koranium Origin unknown. Subspace element used in Klingon warp drives. DS9: Blood Oath - Mentioned briefly as being a part of warp drive in the injectors.
Krieger Waves Artificially generated by aliens. Nature unknown. Eats holes in walls and decks; destroys space station. TNG: A Matter of Perspective - An attempt is made to fashion a power generator using these waves.

L
NAME
DESCRIPTION REFERANCE
Lepton Naturally occuring. - particle "activity" increased prior to the wormhole reappearing and shifting its position. TNG: "The Price" - Geordi's visor detected the "activity".

M
NAME
DESCRIPTION REFERANCE
Meranium Artificially generated by aliens. A metal alloy. Its melting point is 2014 degrees Fahrenheit. TNG: The Vengeance Factor - The away team fired their phasers into the meranium alloy, causing a smoke screen.
Meson Naturally occuring. - particle "activity" increased prior to the wormhole reappearing and shifting its position. TNG: "The Price" - Geordi's visor detected the "activity".
Metrion Artificially generated by aliens. High levels of exposure can infect a humanoid with nitremia, a blood disease that causes its victims' cells to undergo fission. Voyager: Jetrel - The Hakonians used a "Metrion Cascade" to conquer Rynax, a Talaxian moon.
Microdine Enhancer Used specifically for subspace equipment. It has a variety of functions, and is easily callibrated. Keep away from flame. 3x19cm 

N
NAME
DESCRIPTION REFERANCE
Nanites Artificially generated by crew. Micro-robots that are bred for specific tasks; able in some instances to reproduce to collectively form a consciousness. TNG: - Part of Wesley's science experiment that got loose and eventually developed into an advanced civilization.
TNG: - Beverly Crusher thought that a destructive breed could be introduced into the Borg collective.
Neodilithium Naturally occuring. A different form of dilithium. Voyager: Threshold - It was used to take Tom Paris to warp ten, after which he turned into a giant salamander.
Neutron Radiation Naturally occuring. Neutrons are neutral particles which, along with protons, are constituents of atomic nuclei.  Neutrons not contained within a nucleus have a half-life of about 15 minutes. Movie: Star Trek VI - The improved Bird-of-Prey gave off a surge of neutron radiation just before it fired a photon torpedo.
Nitrium Naturally occuring. A metal used in an important alloy commonly found in starships. The alloy is used for computers, replicators, stabilizers, ventilators, power transfer conduits, dilithium chamber walls, and life support systems. TNG: The Cost of Living - Nitrium parasites started feeding on the ship's systems after the Enterprise destoyed their nitrium-rich asteroid. The parasites digested much of the Enterprise's nitrium into slime before Data lured them back onto the asteroids of the Peloris Field.
Nucleogenic Naturally occuring. Dust or other particles which attract water vapor, causing rain or other precipitation to form. Voyager: The Caretaker - The Ocampa homeworld's atmosphere didn't have any, which accounted for its desolate condition.
Nucleonic Radiation Naturally occuring/artificially generated by crew. Something found in lifeforms. Voyager: The Cloud - Used to make a suture to seal up the punctured nebula creature.

O
NAME
DESCRIPTION REFERANCE
Omicron Naturally occuring. Created by Space Nebula Creature, used in "circulatory" system. Voyager: The Cloud - Thought to be a substitute for anti-matter for the warp drives, as well as fuel for the replicators.
DS9: Shadow Play - Emitted by holographic generator. The projections/people were "made of" them.
Voyager: Nemesis - Chakotay was conducting a survey mission to a planet with a high concentration of omicron particles in the atmosphere when his shuttle came under attack.

P
NAME
DESCRIPTION REFERANCE
Particle Signature Naturally occuring. A characteristic unique to each universe. TNG: Parallels - Used to prove that Worf was indeed in an alternate universe and find the correct universe to return him to.
Pergium Naturally occuring. Used to regenerate enviromental controls filters. Voyager: Fair Trade - Janeway listed "pergium" as one of the needs that Voyager was to barter for.  Submitted with other requests to the space station's manager.
TOS: Devil in the Dark - The crew beams down to a planet that mines pergium for the Federation, to investigate the recent deaths of several pergium miners.
Plasma Naturally occuring. A very hot, ionized gas. The atoms in plasma have enough kinetic energy that the electrons are torn from their nuclei, ionizing the gas. Movie: Star Trek VI: The Undiscovered Country - Plasma emissions were used to detect a cloaked Klingon Bird of Prey.
Promethean Quartz Naturally occuring. Valuable mineral that glows with an internal light. DS9: Q-Less - Vash discovered a similar geode resembling Promethean quartz in the Gamma Quadrant and nearly destroyed the station with a graviton field.
Pulse Compression Wave Artificially generated by crew. Used to increase the power of a phaser blast. DS9: Emissary - Used to increase the power of DS9's phasers against Gul Jassad's fleet.

Q
NAME
DESCRIPTION REFERANCE
Quantum Filament Naturally occuring. An enlongated subatomic object, hundreds of meters long, but possessing almost no mass. TNG: Disaster - Caused damage to the ship. Troi asked O'Brien if a quantum filament was a kind of cosmic string; O'Brien said it was something completely different.
Quantum Regulator This tool is used to work with quantum fluctuations, quantum regularities, and a useful tool in field mechanics. This tool is rather small, and hand held. 23cm long with a thin, rod shaped, rounded tip.

R
NAME
DESCRIPTION REFERANCE
Rubindium Origin unknown. A nontoxic crystalline substance. TOS: Patterns Of Force - Rubindium crystals are component elements of starfleet subcutaneous transponders. Kirk and Spock have these monitoring devices inserted into them, but upon capture they use the crystals to generate a primitive laser.

S
NAME
DESCRIPTION REFERANCE
Sarium Origin unknown. Can store large amounts of energy. TNG: In Theory - Sarium was mentioned as being vital to the engines of Federation shuttlecraft.
Soliton Wave In real life, a wave whose energy doesn't diminish. (More complicated than that, but that's the basic idea.) In Star Trek, an artificially generated subspace effect capable of propelling vessels at warp speeds. TNG: New Ground - Enterprise participates in a test of their use as a propulsion system.
Static Warp Bubble Artificially generated by crew. An anomaly which creates a new universe whose nature can be affected by the individual trapped inside. TNG: Remember Me - Beverly was stuck in one and Wesley and the Traveler had to get her out.
Steelplast Artificially generated by aliens. A construction material. TNG: Too Short a Season - In the tunnels of Mordan IV, the away team ran into a dead end, where a tunnel used to be. Geordi's visor indicated the sealent as steelplast, which was recently installed.
Styrolite Artificially generated by crew. A non-opaque particle used in packaging. It is biologically sterile and can be used to package potentionaly biologically hazardous substances. TNG: Unnatural Selection - To contain a person in suspended animation for medical examination without threat of contagion.

T
NAME
DESCRIPTION REFERANCE
Talgonite Artificially generated by aliens. A ceramic substance. TNG: The Inner Light - Used in the construction of the Kataan probe.
Tellerium Origin unknown. Crystal used to stabilise the harmonic reactions inside the dilithium chamber of Voyager's matter/antimatter power reactor. Voyager: Resistance - Janeway is wounded while Tuvok and Torres are taken prisioners by the Mokra, a tyranic military regime, during a desperate expedition to find tellerium.
Terminium Origin unknown. A metal alloy. Movie: The Search for Spock - Used in casing of photon torpedoes.
Tetralubisol Origin unknown. Highly volatile lubricant used on starships. TOS: The Concience of the King - Lenore Karidian attempted to kill Kevin Riley by poisoning his milk with tetralubisol.
Thoron Naturally occuring. Radioactive isotope by-product from the decay of thorium. Thorium is also known as radon-220. DS9: If Wishes Were Horses - Elevated thoron emissions accompanied the appearance of aliens in the Denorios Belt.
DS9: The Emissary - A thoron field was used as a shield against Cardassian sensors by the crew of DS9 to hide the true strength of the station.
Transparent Aluminum Artificially generated by crew. Just what the name implies, a clear metal. Movie: The Voyage Home - Scotty showed a scientist how to make it, in exchange for a supply of plexiglas to build a whale tank.
Tritium Naturally occuring. A radioactive isotope of hydrogen with atoms of three times the mass of ordinary light hydrogen atoms. TOS: Operation -- Annihilate! - (See trimagnesite.)
DS9: Q-Less - Used by Dax and O'Brien to trace the origins of the gravimetric disturbances.

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Verdion Naturally occuring. Generated in the cores or surfaces of White Dwarfs. I really wonder if the writers even know what a white dwarf is... TNG: Emergence - Made Living Organisms. As mentioned earlier was needed for the Enterprise to grow.
TNG: The Pegasus - They used a wash of Vertion particles to hide the Pegasus from a Romulan ship.
Veridium Artificially generated by crew. Can be detected at great distances, except through a magnetic shield. Movie: The Undiscovered Country - Spock places a veridium patch on Kirk's shoulder so the Enterprise can find them upon emergence from the magnetic shield.
Verteron Artificially generated by aliens. Somehow damaging to sub-space equipment (not the same as 'vertion'). TNG: Force of Nature - A generator of these, disguised as a bouy, is used by environmentalists to incapacitate several ships, including the Enterprise.
DS9: Playing God - Threatened to destroy the proto-universe.
Voyager: Eye of the Needle - Captain Janeway pointed out that there were "...verteron emanations, tunneling secondary particles. It certainly looks like a wormhole..."
DS9: In The Hands of the Prophets - Keiko was explaining to her class at the beginning of the episode that this is what the Bajoran wormhole is made out of before Vedek Winn came in to complain about the absence of "creationist" theory in the classroom.
Victurium Alloy Artificially generated by crew. A very dense metal alloy. TNG: Hero Worship - Large amounts of it blocked the transporter.

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Warp Core matrix flux capacitor Used for power distribution of the EPS. Can be easily callibrated to adjust any warp core. Dimensions are roughly the same as a Microdine Enhancer.
Warp Particle Artificially generated by crew. Emitted by warp engines. Voyager: Parallax - Evidence of the Voyager's path in the singularity.
Warp Shell Artificially generated by crew. A field generated by the Enterprise's engines to induce warp travel. TNG: All Good Things - Picard used static warp shells to seal the temporal rifts in the three time instances.
Wormholes Naturally occuring. A subspace bridge or tunnel between two points in "normal" time and space. Most wormholes are extremely unstable and their end points fluctulate widely across time and space. An improperly balanced warp drive system can create an artifical wormhole that can pose a serious danger to the ship and its crew. DS9 - The only known stable wormhole, leading to the Gamma Quadrant, is right next to the station, lending DS9 its strategic importance to the Federation.
TNG: The Price - The Enterprise-D encountered one and their mission was to study it.
Movie: The Motion Picture - The Enterprise gets caught in a wormhole due to an warp engine imbalance.

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Z Particle Artificially generated by aliens; also a real type of particle. Can mess up sensor and/or visual records. In real life: today's understanding puts particles into two basic categories, matter and exchange particles. Exchange particles are thrown kind of like frisbees between matter particles as the generators of the forces. Photons mediate the electromagnetic force, gluons mediate the strong force, the graviton is proposed (not observed) to mediate the gravitational force. The weak force is mediated by the W+, W-, and Z0 particles. TNG: Devil's Due - Scientist on Ventax II station detected Z-particles coming from Ardra's ship.
TNG: Identity Crisis - LaForge initiated a scan for "Z-Particle emissions" on the video recording of the Tarchannen III mission.
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