I guess my vote goes for Penance. You have to know exactly what you're doing and take care of his arms, or else you're doomed. Omega Weapon from FFVIII was hard, but I didn't have that much trouble with him.
By the way, Spee, if you would have added Emerald/Ruby Weapon from FFVII to the poll, they would definitely have gotten my vote. They were rock-hard. Emerald was hard and fun, but Ruby was just hard. What on earth? Come to the battle with two characters killed, or they will be thrown out of battle. What kind of a moron comes up with an idea like that?!