@Senshi:
Kingdom Hearts:
Fighting Sephiroth!
He's not too hard if you can stop Sin Harvest, and goes in with a full stash of elixers.
I have to 4th Jinpachi. I don't know HOW long it took me to defeat him with Paul…damn me for setting a fight to two rounds.
Other than that, Challenge of the Gods in God of War, as well as God mode, are tough as hell. As are the Dark Aeons in FFX; I still haven't defeated Anima, Magus sisters and Penance.
Oh, and the old geezer at the bottom of Via infinitio in FFX-2 was a pain as well...