
"Favorite" isn't the word really for me because all bosses fill me with dread as I enter upon their lair. My least favorite then is the one I'm working on now in Enchanted Arms. It's multiple bosses, one after another without a break, and each changes into alternate forms to make you fight them again. Epicly painful!
My next least favorite is Weapon-X in X-Men Origins: Wolverine. That's a boss type that incorporates all the abilities of previous bosses for the ultimate challenge. He was a bastard, but I beat 'em.
Finally there's the hunter Shaw in Open Season who you've been thinking about the whole game and finally face in the last level. It's neat to have a boss that's kind of ever present in a game, but who you don't meet until the end. It gives the game a movie like quality and really builds the tension. Luckily I was a big ol' bear in the game and gave that hunter a big ol' bite for the win. Still, he was a pain in the paw.