Either Seymour from FFX, Sephiroth from KH, or Lloyd from Legend of the Dragoon (though I'd like to nominate a lot of bosses from that game. Emperor Doyle destroyed my ego as a kid). I'd like it to be known that most prettyboys from a JRPG are hard as hell.
Others include the Armadillo from Ninja Gaiden 2 (especially the double up fight. YOU DIDN'T GIVE ME ANY INDICTATION THAT I SHOULD BLOCK A F*CKING BLAST THAT WOULD LEVEL A CITY!!!), any small swarming enemy, Yggdrasil from Tales of Symphonia (almost everytime you face him, it's after you fight his weaker, but still very tough subordinates. In fact the first time he is the third boss in a row when the second one is so tough that they made beating him optional), the reapers from RE5 (instakill plus no run-and-gun... not fun), either Odin or Hecatoncheir from FFXIII (and the chapter 10 boss), Unlimited Hakuman from BlazBlue, the first colossus from SotC (this is the guy that will decide whether or not you play the rest of the game or give up), Death Claws from Fallout 3, Final Fantasy X's sinspawn scorpion/centipede thing that you fight on the cliffside, and of course Morrigan's mother from Dragon Age: Origins.