Just for the sake of variety, I'll put my top 5:
1: Dracula from Castlevania III: Dracula's Curse
I've heard it isn't that difficult if you use one of the side-characters, but I played the whole game Trevor-only and I wanted to finish it like that. It was pretty tough, specially considering that they don't give you a checkpoint for continuing at the stairs before Dracula, like every other Castlevania does.
2: Diablo from Diablo II
This was pure pain. Did it solo on my first time and it was hard as hell. Dying again and again by that stupid lightning hose just to try to recover my belongings completely naked didn't help my morale either.
3: Ares from God of War
This one wasn't as difficult as some others in this list (definitely not easy though) but it gets a spot simply because of the part where you have to protect Kratos' family against Kratos clones. Doing that in God diffiiculty almost drove me nuts.
4: Aec' Letec from Baldur's Gate: Tales of the Sword Coast
Pure pain, incarnated. It took me a whole night of re-loading endlessly until I finally vanquisted this beast. The hardest part of this boss fight is that even if you kill the boss, he can take the body of one of the cultists like he is "The Thing".
5: Omega weapon from Final Fantasy VIII
This one I dreamt of beating when I was a child, but I could only stand against it when I replayed the game a few years ago. Even with my best team, the best magic equipped and a good strategy, I'd say that I only managed to beat it by pure luck. I didn't use the invulnerability items cause I wanted to make it as hard as possible.
