It's really easy to find hard bosses if you look to the NES/SNES. The first one that comes to mind for me is N'astirh from Spider-Man/X-Men: Arcade's Revenge. Even if you took out the bosses that game is next to impossible.

I remember the final boss for Kingdom Hearts 1 was really hard too. I never beat it.

Final Fantasy series is full of them too.

[QQQQ]

The Head Thwomp in Oracle of Ages. I spent weeks trying to beat that thing the first time. Luckily the timing is now ingrained into my skull, but for a while it looked impossible.

In terms of video game storybuilding rather than difficult fights--Red Pyramid Thing fight from Silent Hill 2.

You never win

-Janus

The final boss on that Spiderman 64 game. It was a (spoiler alert!) fusion of Doctor Octopus and Carnage, and it took me a very long time to beat it.

Oh, and Queen Gohma from Ocarina of Time.

Seriously, she was the first Zelda boss I ever faced, and I had no idea what to do, so I just ran around in circles until I got killed... :\

For me, Gyorg in Majora's Mask.

Not only is it hard to hit him without getting damage, he can easily out-swim you if you mess up and take off a whopping two hearts.

I HATE YOU GYORG. Especially since I'm trying to beat the game with only three hearts.

And this one's not really hard, but it took me FOREVER to figure out how to beat King Bob-obm in Super Mario 64. How was I supposed to know you were only supposed to drop him on the top of the mountain? Throwing him off the peak made much more sense to me....

The Lich King in World of Warcraft --owait, still a few days before he is able to be killed

I remember the final boss for Kingdom Hearts 1 was really hard too. I never beat it.

 

[QQQQ]

Xemnas in KH 2 is even harder in my opinion.I mean you have to deflect thousands of lasers at the on time.

Boom,headshot.

Hmm... not to many games played to say. I could bring up Duncan the Black from Guild Wars in Hard Mode, but that's still not that tough, just time consuming. Borderlands has no particularly tough bosses... both Elder Scrolls games I've played are fairly easy. Morrowinds expansion, Bloodmoon, has a pretty hard boss if you play on Max Difficulty, but Oblivion is pretty easy as far as BOSSES are concerned.

Haven't played Knights of the Old Republic enough within the last few years. Last time I played I was 10 or 11, and nothing was too hard. The last boss was pretty tough though, he took a lot of time and effort to get down. But still not really that bad... I would have to say the hardest boss I've ever fought was... my mother. Level (Infinity) monster with (Infinity) hit points and an (Infinity) damage attack called "Clean your room!".

-Levacius Zehvor

The Lich King in World of Warcraft --owait, still a few days before he is able to be killed

Ok, guaranteed he is extremely hard because he is defeatable now, and it is a very tough group effort.