Good: Dante in DMC4 midway through the game, when you were playing as Nero. That fight kicked my ass so many times until I got a proper rhythm going. He came at you like he was an actual played character, utilising all of his abilities and being really cheap about some of them

Also I'm gonna back up the Saren vote. Part of me was compelled by the whole "Submission is preferable to annihilation" argument.
Bad: Timeshift final battle. I just found that thoroughly underwhelming. They have you on a building roof shooting at this far away giant robot. I never felt connected to the fight though. More like an annoying pest. It wasn't fun for me, and barely felt like a boss by the time I'd won.
Also, Atlas from Bioshock. The fight, as opposed to the character. The ending too which followed. I felt utterly underwhelmed from the start of the fight til the end of the credits roll.
Ugly: 343 Guilty Spark on Halo 3. I'm sorry, I thought the last boss was meant to be CHALLENGING.
Really ugly: Any and all dark Aeons+Penance(sp?) from FFX. Fuck those fights, seriously. -_-