So many good ones. I won't list anything I've seen elsewhere on the thread to keep this from being a mile long.
4. Ghost Trick: Phantom Detective: Ghost Trick is an idealized SNES era adventure-puzzle game, and the soundtrack captures that feel perfectly.
3. Final Fantasy XIII-2: They techno-riff most of their own themes.
2. Legend of Zelda: Majora's Mask: Zelda always has great music, but Majora really went for the dissonant and dark side, which I'm a complete sucker for.
1. Parasite Eve: The antagonist is a mutated opera singer. I really don't think there's anything else I can add.