Sephiroth from Kingdom Hearts was ridiculously difficult. I got past his attack that brings your HP and MP down to 1, but when he's at 2/3 of his health, he starts using attacks that are almost impossible to dodge. Plus, he doesn't forget about his other attacks and makes sure to play keep-away from you while you're getting hit. Then he doesn't give you anything (except for XP, which you don't need anymore at this point) for killing him!
Redrum from Xenogears was difficult if you didn't have three hours to sit and wait for non-combos to kill him. This is due to his killing off whoever hits him with a Death Blow. And there was NO WAY TO DEFEND AGAINST IT! Pretty much, if you're going to fight him, make sure you have the entire day to do so. (Murder is Redrum and Redrum is Murder... Heh heh...)
I'll post more soon.