Pshaw you guys have it easy. The hardest boss in gaming history is the Demi Fiend from Digital Devil Saga. TV Tropes describes it best:
The Demi-Fiend battle in Digital Devil Saga, quite possibly one of the hardest bosses in the history of JRPGs, if not the hardest boss. Not only will he instantly kill you in the first turn if you have a "forbidden" move set, but the strategy required to defeat him requires a very specific use of one usually worthless skill that you would never use in the main game. I have no clue how anyone could figure this out without the use of a strategy guide. Beating him gets you a useful accessory that you can only use in the sequel. And even then, if you do manage to get him down to half health, his High Pixie will fully heal him. If you kill all of his demon companions, he'll insta-kill you. If you go in with any negating moves (the said 'forbidden list'), he'll insta-kill you. Hell, even with the correct strategy, if you take too long to kill him, he'll just get bored and insta-kill you anyway. To add insult to injury, his battle music is the regular Nocturne battle music, so he may be an uber hard bonus fight to you, but you're nothing more than a random encounter to him. Anyway, even without his instant kill skills, he is beastly difficult ? you need to cap out your major stats to even have a fighting chance, and then there's the actual strategy involved... which simply fails half the time due to bad luck.
Dark Souls wishes it had a boss like this.