Final battle themes? Hmm, let's see ... Chrono Trigger and Earthbound, yeah, for sure. Never made it as far as the final battle in FF9 because my "this is dumb" senses kicked in before then. FF3's is awesome, don't get me wrong, but there are even better ones; I like it but it wouldn't crack a top five list, you know? I'd add Etrian Odyssey 3 for sure, and maybe Lunar: Silver Star Story Complete and Final Fantasy: Mystic Quest (it had good music, shut up.) If I'm allowed to nominate non-RPGs, the final operation in Trauma Center: Under the Knife 2 had a badass endboss theme (what? That series isn't exactly known for its realistic depiction of surgery, so yes a combat-oriented endboss type song for the final operation is appropriate. Here's proof, assuming you don't mind spoiling the final operation in that game.)