-Final Area-
FFII - Castle Pandaemonium (Weird, I know, but I really dug that song, at least the GBA version)
FFVIII - Ulti's Castle
FFIX - Memoria
FFX-2 - Abyss of the Farplane

-Final Boss-
Metroid Prime 2 - Final form of Emperor Ing (I don't know what the song's called, but it's badass)
FFVIII - First form of Ultimecia (I know it played when fighting all the other sorceresses, too, but I love it)
FFIX - Necron
FFX - Yu Yevon