Off the top of my head the two best overall soundtracks I can think of are
1. Final Fantasy VI (SNES, GBA)
2. Jet Force Gemini (N64)
Both are impressive in their composition, and in how they use the hardware. Neither of them use pre-rendered music, like in many modern games.
Zelda 64 made good use of non-prerendered music too, like in the overworld theme. I can't think of many other games that use that technique of music changing depending on what you're doing in the game.
Also, the Metal Gear Solid series have pretty good soundtracks, even if the music isn't often incorporated in the game, more in cutscenes.