3. FF9. Party vs. Trance Kuja in the second last battle of the game. The way it ended was just wow (SPOILER)He casts Ultima. Blows everything up xD. Also the battle itself is pretty fun.
2. FFX-2. Yuripa vs. Vegnagun -> Shuyin. A great series of boss battles. Criticise the game all you want but I really like how this battle was done. I found the idea of Vegnagun being controlled by a super-organ to be really...neat xD.
1. The Bouncer. Sion, Volt and Kou vs. Dauragon. This battle frustrated me to no end. Dauragon is just so damn beef. Just when you think you've got him, he strips down a little bit more and comes back with full health and an extra move of ultimate-pwnage. Words cannot describe just how bad you feel when you lose and just how good you feel when you win.