Since the software and technology changed over time, I don't know of a simple answer to your question. It varied from game to game and track to track, and even varied within a single track from what I understand. For instance, in "One Winged Angel" I believe he used redbook audio to record the choral parts. But the rest of the song was recorded with a series of different and comparatively primitive synthesizers. Others probably know a lot more about the technical side of things. I'm gonna plead ignorance, although it's something that interests me.
However, you could ask the man himself through his website:
http://www.square-enix-usa.com/uematsu/
Also, for more general information on the software and technology (and the history of its advances):
http://en.wikipedia.org/wiki/Computer_and_video_game_music
http://www.vgmusic.com/vgpaper.shtml