Jet Force Gemini. Especially Title Screen and Character Select are forever stuck in my head.

https://www.youtube.com/watch?v=BYi8o-RAWuk&list=PLQhKXYgOXl3sUPNGhM3rYyTtk7fwkumUL

Persona 4 GOLDEN or Final Fantasy XIII. Too hard to choose between the two.

Hitman: Blood Money bar none. The atmosphere it set on every level was incredible.

Age of Conan

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.

Ys Book I & II

Ys III: Wanderers from Ys

Ys IV: The Dawn of Ys

Super Mario 64

The Legend of Zelda: Ocarina of Time

Soldner-X 2: Final Prototype

DuckTales: Remastered

Donkey Kong Country

Jesus, I don't know that I can choose. I'll just toss in some honourable mentions:

Final Fantasy series, with 4, 6, and 7 being pretty high on the list.
Ys series, with 1 and 3 (and Oath) being high on the list
Castlevania series
Metroid Prime series
Zelda: A Link to the Past