Here's a quick list of my favorite video game soundtracks for each generation since I started playing (not including current generation--can't pick a favorite if there's still new stuff coming out, plus I haven't actually played any games from the current generation).
8-bit: Mega Man 2, Takashi Tateishi: C'mon. That intro? Wily 1? Does this even have competition?
Honorable Mention: Yes, it does. Ducktales.
16-bit: Final Fantasy VI, Nobuo Uematsu: Another one with little in the way of competition. The Opera House sequence was like half an hour of kinda-crappy gameplay not only redeemed, but rendered classic, by the SNES sound chip being made to do things it had never done before--and then that glorious ending! Not to mention some truly outstanding character themes in between, such as Kefka's, Celes', and Cyan's, and of course the utterly haunting world map and incredible second airship theme... I could go on like this.
Honorable Mentions: Chronotrigger, particularly when you know it was Mitsuda's first professional job. (We'll be seeing him again shortly.) Mega Man X.
PSX/N64/Dreamcast: Xenogears, Yasunori Mitsuda. Holy crap yes, from the vaguely Celtic-sounding "Aveh--Ancient Dance" to the Arab-flavored "Dajil--City of Burning Sands," the ethereal majesty of "The Beginning and the End" to whatever the hell (other than FRICKING AWESOME) "Awakening" was, this was the game that announced Mitsuda as someone to pay attention to (since Uematsu kind of ganked the credit for Chronotrigger.)
Honorable Mentions: Lunar: The Silver Star, a fun, energetic, and sprightly sound perfectly fitted to its pre-FF7 largely-angstless RPG aesthetic. Chrono Cross, another Mitsuda work, and the polar opposite of Lunar, a soundtrack that utterly doesn't fit the game at all as a consequence of being, y'know, actually good. The Legend of Zelda: Majora's Mask, much like the game itself, went for a weirder and darker tone than the safe path followed by Ocarina, and (again, like the game itself) ends up the stronger work as a result. Final Fantasy 8, despite being nigh-universally (and rightfully) reviled for its easily breakable gameplay, uninteresting cast, and convoluted story, is Uematsu's best post-SNES work.
PS2/GameCube/X-Box: Xenosaga, Yasunori Mitsuda (Episode 1) and Yuki Kajiura (Episodes 2 and 3). Okay, yeah, I'm cheating and giving it to the whole franchise, but it's the only way to get someone other than Mitsuda some space, because his bombastic, operatic soundtrack for Episode 1 is both a perfect fit for the game's vast scope (and, let's be honest, joyous pretention) and an excellent listen on its own, reusing and expanding upon certain key themes from Xenogears in ways that transcend that game's soundtrack. Yuki Kajiura, on the other hand, does the second-best work of her career to date (only Madoka Magica is better) on the next two games of the series, including particular standouts "Image Theme" and "Communication Breakdown" from Episode 2 and "Godsibb" from Episode 3.
Honorable Mentions: Legend of Zelda: The Wind Waker is the only one I can think of. This is the generation where my gaming time began to shrink.
PS3/Wii/X-Box 360: Smash Bros. Brawl. Yeah, I am completely cheating, since the soundtrack is almost entirely made of remixes. But they're good remixes of tracks that deserve to be remixed!
Honorable Mentions: None. This is the generation where my gaming time vanished entirely.