The opening sequence in Full Throttle, though really, the entire game should qualify. This troper tracked down the Gone Jackal's only album entirely because of "Legacy". This troper is also looking forward to Brutal Legend because anyone with an ear for a great soundtrack in the past has got to be good at making an entire game based on music itself.
Knights of the Old Republic deserves some mention. Of course, it's Star Wars, so along with the Obligatory Epic Lightsaber Fight Scene comes the Obligatory Epic Lightsaber FightMusic. But there's also the Infinite Fleet Theme - so-named because the final cinematic for the Dark Side ending pans out through a fleet (a big fleet) of Sith destroyers ready to conquer the galaxy.
Oh we did NOT just get this far without mentioning the utterly awesome music that plays during the character creation screne, The Old Republic
The iMUSE interactive MIDI system definitely proved its worth for its utilization of a format that is generally regarded as having lackluster sampling in the games that made use of it, and the soundtracks themselves certainly contributed to the experience as well. Dark Forces boasts a remarkable score all around, with noteworthy tracks played during cutscenes that show Kyle in transit to Anteevy/escaping from his captor's ship or making his escape after blowing something up. The music scored for TIE Fighter likewise has an excellent variety to offer, but perhaps the most memorable comes from the opening cinematic (particularly towards the end where the Imperials pursue the fleeing Rebels). Regrettably, the original score was replaced with the music (or perhaps remixes thereof) from the original movie trilogy's soundtracks in later releases of the compilation CD.
The remix for the Collector's Edition isn't anything to sneeze at, either.
While later installment mostly used tracks from the films, the first Dark Forces game had a truly badass original theme.