Prelude
Probably VIII, gonna hafta get back to ya on that one.

Main FF Theme
IV, when it plays right before the final dungeon

Battle Theme
V or IX, can't decide. Both pretty awesome

Fanfare
XII, it even comes with a nice congratulations flashing on the screen.

Game Over
IX, dunno why. I just liked IX's game over music.

Boss Battle
Mystic Quest, loved the boss music. Especially the final boss'

Chocobo
FFVIII, loved it. Fun running around the Disc 4 music with that playing.

Town *NEW*
V, I loved the towns that had the Celtic type music playing.