Duke Nukem Forever's final boss. Although I have to wonder if they didn't do it deliberately.
Being fair the final boss has to be beatable within the constraints of the game's established mechanics. This makes it very hard to make an epic boss battle because you HAVE to take 'em down using stuff you've been doing all through the game, which makes it feel cheap when you do kill 'em because, well, they're the END BOSS, right? They shouldn't be harmed by normal attacks!
If they're just people, why not?
Sometimes final bosses are done pretty well within the mechanics of the game. For example, the final 'boss' of Half-Life 2 isn't really a boss, but being forced to use the gravity gun adds a different level of difficulty to it depending on how much practice you had with it previously. Portals 1 & 2 have 'boss' fights that are more a series of timed puzzles than actual 'boss fights' and so retain the satisfaction of solving the puzzles while also introducing a ton of tension. Plus, what endings! I also seem to recall Shadow of the Colossus' end boss being breathtakingly, terrifyingly epic >>
As for my biggest end boss 'What?' moment, I'd say the end boss of FF9. You chinned Kuja easily... And then a giant floating crystal turns up exclaiming that you've 'FOIELD HIS PLANZORZ!!1!!1111!!'... I was like 'Who the hell are you?' -.- and waltzed all over him too