I have a soft spot for the music in Deus Ex. It's mostly old synth sounds, but it really fit the game perfectly, which is what you want from a soundtrack.
Some other good ones:
Planescape: Torment
Fallout
Fallout 3
World of Warcraft (the parts that don't have a fake-Latin chorus, which I hate)
Sim City 4
Civilization IV (it's all good, but the original music used as the main theme, "Baba Yetu", is an especially good piece)
Tropico
KOTOR
Morrowind (could have used a bit more music, but what was there was good)
Alpha Centauri has a soundtrack that I really like with its gameplay; but as far as I've been able to tell, aside from the opening theme, it is generated by the game from a set of one- and two-note files, along with some very short event pieces.

Composed by Terry Scott Taylor, my musical hero.

Elderscrolls III: Morrowind
Neverwinter Nights
Dungeon Siege
Outcast
Halo-series
Anachronox
Sacrifice
Shadow of the Colossus
Giants: Citizen Kabuto
Wipeout
MDK 2
Command & Conquer
Full Throttle
Dark Forces: Jedi Knight (taken from the movies mostly, but combined with the games setting, it became so much more)
So many more.. also, loved the title song from the first Tomb Raider. Listened to it over and over.
EDIT: Had to add Dungeon Siege... I'm such a sucker for Jeremy Soule...

Rob King - Might And Magic 6-8 !!!!!
Age Of Conan:
http://www.youtube.com/watch?v=2zMBCpCwnbo&feature=channel_page

Off the top of my head I can only think of:
Dream Web
System Shock 2

One of the best game soundtrack I've heard these years is the one from Shadow of the Colossus. A very special music for a very special game.
And I'll never be bored of listening any Nobuo Uematsu music. This composer is a real genius, I still wonder how he can compose so many great themes per game.

Having just listened to the soundtrack from Beyond Good & Evil, I think that'd have to rank up there with the best, never heard such a varied game soundtrack before.
Braid also has an amazing soundtrack, it just blended so perfectly with the game. Then again the game is cut from 24 carat style so I'd expect nothing else
Messiah had Fear Factory so thats an instant level of awesome
Does GTA's radio stations count as a soundtrack? If so, the ones from GTA4 and The Lost And Damned are really good for setting trhe feel of the city and story (and TLAD making Liberty City Hardcore actually GOOD rather than tryhard bullshit was a major improvement)
All the games by Telltale have excellent music that really backs up the feel of the game (well I can't really say that since I've not played the strongbad games but its a save assumption)

The old Amiga was really an incredible computer for game sound effects and music, at its time.
Chaos Engine has indeed a great soundtrack, as well as the opening theme of Speedball II (also from The Bitmap Brothers).
But my favourite Amiga game soundtrack is without any doubt Turrican II, by Chris Hülsbeck. A real piece of art, and still excellent electro music.

Silent Hill series - soundtracks are superior to any other.
Then Max Payne, Bioshock, Fallout 3, Morrowind, Xenosaga maybe

Deus Ex
Fallout 2
Fallout 1
Total Annihilation
Syndicate Wars
X-Com: Enemy Unknown AGA version.
X-Com: Apocalypse.
In that order.

Bioshock
Shadow Hearts series
NiGHTS series
Rayman (the first)
Alone in the Dark (2008) - Olivier Deriviere rocks
Final Fantasy series
Chrono Cross
Chrono Trigger
Xenogears
Xenosaga series
Tomb Raider series
Broken Sword 1 and 2 (never played the others)
Metal Gear Solid series
Folklore
Shadow of the colossus
I'm sure there are more...

Oblivion, Oblivion, Oblivion
The game's shit, but the music is outstanding.

Yes, Beth also loved it. So much they decided to re-use it in Fallout 3.
For some reason i really liked the soundtrack of 'Experience 112'. And it was a chore to find an extractor able to handle the damn ARC files to browse trough the sound.
Some tracks from Dreamfall and VTMB also caught my attention because they really fit with the game/scene mood.

I like to differentiate b/t "Licensed Music" and "Traditional Scores."
When GTA has like 400 different songs, I see that as "Licensed Music."
There's nothing new or original normally in the GTA games for music that they composed -- they get licenses to use other artist's music (for the most part).
Brand new music by an orchestra that you hear composed by Inon Zur for numerous game-- well, there's a long list of games he's scored; see Fallout 3, Prince of Persia (2008), Syberia 2, BG2: TOB Expansion, Icewind Dale 2, Crysis -- I see that all as a "Traditional Score."
It's worth noting that some games -- see Vampire: Bloodlines -- have both strong "Licensed Music" (songs licensed from other artist's albums -- music by Chiasm, Lacuna Coil, Genitorturers, etc etc) and a whole nice strong "Traditional Score" (which was composed by The Womb Music Group).
Oh, I should note -- I really loved the score for Arcanum.

Super Castlevania IV
Castlevania Symphony of the Night
Super Metroid
Turrican II
Unreal
Unreal Tournament
..are some of my favourites