The one from FF9
The one from Yoshi's Island on the SNES
The one from Guilty Gear (Meet Again)
The one from Guilty Gear X (Awe of She)
And the one from uh... well I'm not sure. I'll get back to you on that one. Does "Bark At The Moon" in the first Guitar Hero count as a final boss theme? As much as I hate Ozzy, I loved closing the game with this song.

I'm glad to see someone beat me to the punch on Yoshi's Island there as well!