Shadowrun for SNES had a pretty fantastic soundtrack. It did a lot with very little and really paints a picture of the setting very quickly. Another candidate from the same era is Planescape: Torment. It had this great haunting ambient sound that made Sigil feel so strange and ancient.
At the time though, if you'd asked me which game had the best soundtrack, I've had pointed to Tony Hawk, though I'm not sure if it was 1 or 2. The one with Party at Ground Zero. Found some great music of the era that way!