Honestly I don't remember. It wasn't the hardest boss I've ever faced, even in just that game, it was just really frustrating. Now that I think about it the controls probably contributed to 99% of the frustration. I adore AOD as I do ALL of the Raider games but it is without a doubt the weakest in the series because of the sluggish controls.

I'm trying to remember the bug boss. I blacked out all the boss battles from that game. :P

EDIT: I REMEBER!!!!!
You had to shoot out it's glands/sacks/whatever before you could kill it. That did suck and it did take me the better part of a day. I think I eventually figured out a way to keep side stepping so that my aim never left the sacks and I was able to blast them off relatively quickly, then it was all cake from there.

Vader in Force Unleashed. Made me quit the game but to be honest it was just the last drop as I wanted to quit before that.

I'll give my vote also to the Final Fantasy 7 superbosses, mainly the "Ruby Weapon" (I think). The nice thing was that they were optional bosses, but of course I wanted to beat them.

I am unsure if I could have ever come up with a way to beat Ruby Weapon on my own. It just seemed impossible.

So I resorted to some walkthroughs, and the ways they gave in them to beat e.g. Ruby Weapon were quite complicated, daisy-chaining different hard-to-get spells and such. And some of the suggestions didn't even seem to work for me, even though the walkthrough claimed that with the suggested mix of spells (including "mimic"), you can just leave the game and your party will eventually kill the boss on their own. Nope, didn't work, my party still died in no time.

Then some suggestions were quite odd, as if they were trying to trick the game. Or was the intention of the game designers really so that you should kill one or two of your party members yourself in the beginning of the fight, in order to beat the boss? It seemed like that was just using some glitch in the game logic to its advantage.

I don't recall how I finally beat Ruby Weapon, but I recall it was not easy, even with clear instructions. I was playing the PC version (the earlier one, not the remake), if that matters.

FFXI: Pandemonium Warden

A Linkshell fought him for 18+ hours and wasn't able to beat him.

Some JRPG super bosses come to mind.

Dullahan from Golden Sun: The Lost Age was a nightmare to go through, attacks 2-3 times per turn (which includes the Djinn Storm attack that cripples your entire party, the Charon summon that sometimes instant kills one of your party members and does massive damage to your other ones, constantly casting curse on your party members, and recovers some health after certain attacks). At least he has a pattern that you can see and prepare for, but unless you're at the max level and can heal quickly the battle will be over rather fast.

Deadbeard from the first Golden Sun is considered a superboss, but he really isn't as cheap as Dullahan. He still packs quite a punch and unless you're prepared you'll be dead very quickly (unless you're somehow at the max level).

Omega and Shinryu from Final Fantasy 5 come to mind as well. Only got to beat them from doing as much damage as possible before they killed my entire party.

And of course the Emerald and Ruby Weapon from Final Fantasy 7. I've beaten the game...but not these two bastards. High attack power and one of them being on a time limit doesn't help either.

Capra Demon from Dark Souls was so fucking cheap, two dogs doing combos on you while the main boss will finish you off with one hit. Getting rid of those two dogs makes the boss actually manageable, but with them the boss battle is a nightmare.

That's all I can think of at the moment.

Your nemesis of the month it seems ;)
Edit : I have to admit he would have make me crazy if FTL didn't already do so couples of weeks ago.

Back on topic : If I had to chose, it would be in Icewind Dale 2. I'll let you guess who and who.

Ha. Four people going against Duriel from Diablo II. Tough one. (Check out one of the players names, made me chuckle)

http://www.youtube.com/watch?feature=player_embedded&v=sc4frxe0maQ#! (Diablo 2: Duriel on Normal)

Some of the bosses in FFIX were real killer and if I remember correctly, there's three bosses at the same time in the end.
Of course, Dark Souls bosses made me throw my controller out of the window.

Two stand out:

Arkham Asylum (PS3): Poison Ivy - trying to target her while cartwheeling over her henchman. I've gotten close on several occasions (and I know it's really close to the end of the game) but for some reason I just can't finish her off. At 53, it may be the "real clue" that the age/twitch thingy is real ;-)

Phantasmagoria - The end game "dance" between the heroine and her boyfriend. And you have to do some "DOS trickery" to save the game to restart if you fail to do the dance in the correct sequence! Yuck!

Pre-nerf M'uru. I won't go into details because it'll give me flashbacks.

End boss of SF4, Seth I think? so cheap. Depending on the character the only option you had was to use some cheap tactics back at him, or wait for extreme luck for the AI to derp it up and it diminished any sense of accomplishment.

I actually liked the FF7 challenge bosses, though I'm sure I'm repressing some rage as it was so long ago.

Exactly this. This last boss is so much harder than the rest of the game. It's not even that I don't know how to beat him, I just simply can't do it.

It wasn't so bad, after about 100 retries

This I hate : a pleasantly paced game with a huuuuuuuge stepped up final encounter. This is what I call Extremely poor design. I feel your pain, mates.

Final boss in Riptide, its not hard, as you c an't really lose the fight, just very badly designed and will annoy you on your first encounter as you wont know what to do.