It would take too long to actually go through the soundtracks and pick out my favorites. Instead, I'll just list the games/series that produced the most memorable music for me.
Xenogears
Chrono Trigger
--Both Yasunori Mitsuda's work
The Legend of Zelda [all]
Icewind Dale [all]
Baldur's Gate [all]
Final Fantasy [Some, not all, had very good scores.]
DOOM [The leaked Doom was the first game I played on the PC. The music is nothing special today, but in '92 it really got you into the mood to fight some demons.]
There's more, I'm sure.