Well, given that my inability to beat him - and subsequent intense frustration - led me to give up playing the game, I would have to say the first fight with the titular 'Assassin of Kings' in The Witcher 2. Maybe that game does end up having an incredible story, I won't be seeing it because the combat is... just awful.
I tend not to really play games that feature bosses, as such. Not these days at least. I can chuck a couple of Star Wars examples out though. The first being Jerec at the end of Jedi Knight. Probably wouldn't give me too much grief as an adult, but as 10 year old back when it came out... Jesus Christ! I think the problem I had was an inability to figure out what to do when he did his invincible meditation/healing thing. That and a lack of co-ordination that frequently ended with falling out the central tower, or force jumping to hard (at the time, the fact you could injure yourself by running into a wall with force speed, or smacking your head into the ceiling was a massive source of rage, these days I miss mechanics like that).
My other example would be the level two boss, Kazdan Paratus, in The Force Unleased on Sith Master or whatever the hardest difficulty was called. Holy crap, that would have resulted in a lot of broken controllers if I hadn't emerged from my teen years. Just the worst kind of 'Computer is a cheating asshole' boss fight. You were limited to a tiny portion of an arena he could, and frequently would, just jump right out of. He hit like a truck, blocked whatever you threw at him (which given you had sod all in the way of powers this early in the game, generally wasn't much) and was way, way too fast. Plus he had the old standby of calling in some big mook to beat you up while he was out of the arena and untouchable. One mistake, one single mistake, and those mooks would squish you. I just can't stand gameplay like that.
Eventually, I figured out you could replay the first two levels on the same save and get more XP, so you could max out all the abilities unlocked at that level. Again, not much but it did include this ridiculous combo that not even bosses could block, once you got them in a stunlock loop of sorts. You basically hit them four times, threw them into the air then crashed them back down, leaving you free to hit them while they were on the floor. Hold the block button till they open themselves up, and repeat. Used the technique on every boss for the rest of the game. And that, ladies and gents, is why I hate boss battles. It's always, always simply a matter of finding the one technique that works, amid hours of agony and failed attempts, and spamming it till victory. Booorr-rrriing!