Neutopia has an earlier version of the theme that plays in Yuris Shrine in Neutopia II. I have never heard it actually play in the first game, but it's in there, in all its older-sounding glory.
EDIT: IIRC, that unused track in Exile is supposed to be used outside of the Baiyon(sp?) Tower... the one that collapses when you leave after beating the easiest boss in the whole game. Also, that part in Exile WP where you fight Lawrence... stick around right at the exit for awhile instead of leaving immediately, as the falling rocks will jack up your XP bigtime. When the timer runs out, you'll start to lose health. Leave just before your health completely runs out. You'll have picked up a few thousand free XP in doing this.
EDIT 2: I think there may be an unused track in Vasteel, but my memory is a bit hazy on this one. There's one track on the disc that I could never quite figure out where it went. Whether it's unused or I just have a shit memory is anyone's guess.