I can't recall me absolutly hating a boss. There were some hard bosses I fought, but none brought me to utter rage. Or well, maybe they did once, but not anymore.
Oh wait, you also included past tense in that question. Bosses I used to not like:
-Spikey (Secret of Mana, SNES). When you're not leveling as much as you should, this guy wipes out your party over and over.
-Tarantula (Lufia II, SNES). Same problem as with Spikey, if you don't have enough levels and the proper equipment, this guy is freakishly hard to kill. Summoning minions, having a group-attack that can poison/paralyze teammates, healing spells for himself. Ugh.
I used to not like those two as much, but to go as far as hating them.. no. And aside from that I can't recall antyting. And now that I know tactics, those two aren't a huge pain any longer either.