That One Boss.

[Ovoon]

Star Ocean Till The End of Time, Leaf Wind boss kid thing.

Seriously, you're on your way to kill the dragon god thing, and this little 10 year old boy jumps out from behind the corner. He was 5x harder than the boss, and since it was a directors cut addition, had absolutely no purpose to the story, and said like 2 words. Horrible horrible boss.

 

[Gamblerjoe]

Its hard to think of one in particular, but some of the bosses in Vindictus have extremely cheap attacks. that game in general like to constantly take control away from you and pass it off as a game mechanic. of course, when you are unable to act momentarily, the bosses will immediately single you out of the group.

 

[Rad Party God]

Kingdom Hearts - Olympus Coliseum - Ice Titan & Sephiroth
That and RAAM on the hardest difficulty - I could never find a good enough second player to help me out.

I could actually beat the Ice Titan... after 20 or 30 attempts, if not more. I just never, EVER, defeated Sephirot. Seriously, how was I supposed to even hit that bastard?. I also agree with RAAM, the most difficult boss fight the whole series has ever seen; for shame Epic, how could you make such a shitty boss fight in GOW2?, I still haven't played 3, so I still can make an opinion on that.

Other than that, most recently in Cave Story, trying to beat Ballos. He's the real last boss and it's a nightmare to just get to him, seriously Megaman would be ashamed of himself after playing this level, but the pain doesn't stop there, if you're able to get past that section, you get to fight with the man himself, with his fucking 4 transformations, one harder than the last one.

I've been trying to beat that bastard all week and I just can't...

Also Vergil in DMC3 comes to mind, especially his last boss version.