ridley, super metroid.. was really hard for me
also, the dude in chrono cross (forgot his name) who had the masamune, when you kill him you get the mastermune
also, the last boss of arx fatalis.. he was insanely hard.
EDIT: yeah, the last boss of arx fatalis would use magic to suck you in, then swipe you with his tentacle thingamajiggy..
i had to get all metal gear solid on his ass, hiding behind crap...
if all of that wasnt enough, he summons demons left and right (demons are really kinda hard in that game)