Another vote to Jinpachi.
Also, Kreissack from One Must Fall: 2097.
Every other character has balanced Strength, Agility and Endurance stats, Kreissack has them all maxed out.
He pilots the Nova.
Only bot with an unblockable attack. Called Earthquake Smash, he hits the ground, and if you're not airborne when he does, you fall over and take massive damage. It's his weakest attack, and against several characters, three hits from it will KO them.
And for my flatmate's sake, I have to mention Kingdom Hearts 2. Sephiroth, because, well, he's Sephiroth. He's a sidequest battle which requires a higher level than the final boss fight.
Also, the final boss in that game pulls a rather cheap move when you're about to win. It's the only time the game throws in a new function without pausing until you're ready and fullscreen tutorial. And if you don't work it out in under a minute (this is assuming you're at max level and just healed yourself, it can be over in SECONDS otherwise), you lose. And reset to about 5 or 10 mins of fighting earlier (again depending on your level). And the literally half-hour long buildup is without save points, so if you ragequit, you have to go through it all over again.
Prototype's final boss isn't totally ridiculous, but deserves mention, specifically on hard. Having to do the amount of damage it requires in the time limit before you automatically lose is pretty harsh. As is resetting you to the very start of the fight if you fail. Also, he's mostly just a rehash of a previous boss fight, which was kind of cheap in the other sense of the word.