1. Kefka - A crazy son of a bitch who actually managed to destroy the world.
2. Kuja - As a character I feel like he was the most developed of any FF villain, he had some dastardly plans as well.
3. Sephiroth - WAS IT REALLY SEPHIROTH CONTROLLING THINGS? *massive drama* Anyway, at the least it was Sephiroth (or the memory of him) who was plaguing Cloud's mind, which was a central storyline.
4. Sin - A giant monster of destruction that is also the main character's dad? Yeah, that's enough to make the list for me.
5. Golbez - smurf Zeromus and Square-Enix's last minute 'oh by the way this random guy is the real final boss' plot twists. Why do they always do that? Golbez was the real villain of this game. His severed hand stealing the crystal creeped me out the first time I saw it.