Wow... I'm shocked and somewhat appalled to not see a few of the BITCHIEST bosses ever created up here:
Fatal Frame: It's hard enough having to deal with a frigging camera and a schoolgirl who will go no faster than a fast walk when being chased by ghosts who are out to kill her, but to have to CHARGE the camera by LOOKING at the ghost as it swoops around you this way and that, throwing in various attacks of it's own as you pray that your shot will be a Zero Shot to stun the stupid shit and keep it from taking out HALF YOUR LIFE BAR (because you don't get a single health upgrade, and healing items become so scarce at the end that it's not even funny) it's truly a game that brings my piss to a boil every time I sit down to play. Amazingly well done in the horror, but horrible difficulty curve.
Saphire Weapon (FFXII): Maybe not a true "end boss" as an "after-the-story-is-finished boss", but without the FRICKING thing to make sure that timer goes away, this boss battle litterally is impossible without hacking. I'm absolutely sure of this. Probably.
Conker's Bad Fur Day: "Throw him out the airlock! Throw him out the airlock!" oookaaay... and how do I accomplish this? .... anything...? No..? Okay, time to mash random buttons and see if I can find the right combination to finish this ***** off.
MegaMan 2: Battle Network: Lion Head of fucking DOOM. It took me six grueling months to finally finish that jackass off, only to find that there were more, even MORE powerful shits that I needed to kill.
Need For Speed Carbon: What the hell were they thinking on this one? The guy outruns you EASILLY even with the best gear on your car if you try to take him on. Everything up until that point had been so easy to take down, so long as you knew what you were doing, then suddenly you get a big load of "Fuck you, you lose" handed to you with the final race.
Disappointing bosses:
Dead Space: Shoot the glowing tentacles... woo... so very tough... I let myself die once, just to see what happened. It's a joke how easy that final boss was.
Phantasy Star Online (Gamecube): Note that I never actually played this online, only with friends on my solitary GC... but... whether it was because my friends and I ground that game into a fine dust to snort, leaving me at an unfairly high level, or if it was truly just a horrifically gimped fight... I took the "final boss" of Ep 1 down in about five hits. Let's hear it for the GoBooma's claw.