Well, theres a few
Analogman from Digimon world, for the fact you got to go to the moon and back to kill him, and the bastard just respawns every time
Izunagi from persona 4, i mean, 2 turns one right after another and always attacks everyone!
the last colossus from shadow of the colossus, the thing lasered me so much it took an hour just to get to his feet!, then another 45 minutes to kill him
The Boss on hard from MGS3, really hard to sneak around her, let alone get a round off
Yami from Okami, i mean, he was normal, not to easy, not to hard, but just cheep as hell when it takes all your powers.
and last, my most hated enemy in all of gaming is Ultimecia via FF8, right when you think she is down, another form comes up from nowhere and trys to kill you, i mean, the 1st one is easy, but right when you get to Griver, it gets harder, more so when they start killing your magic