For me, it's a tie between Blizzeta and Stallord. Stallord was challenging and interesting as a boss. Blizzeta wasn't too too hard (althought I died in that battle) Both I loved the ball and chain, so I loved being able to use it in battle. Her boss music was great, too.
Excluding the main baddies, my favorite boss would have to be Stallord. I love his introduction; I love the way in which the Spinner's used during the fight ('tis a shame that it wasn't featured more prominently after that); I love the "twist" that starts the second half of the battle. Zelda needs more boss fights that are as creative as this one.
Twilit Fossil Stallord was my favorite boss in Twilight Princess. This boss game me the most oportunity to use the spinner in unique ways. By the way the spinner is my favorite item.
I always likes the minibosses more than the bosses, and in this case I like Ook and Darkhammer, and the last of them I love because the first time I played I just couldn't make it, he just killed me over and over again. But I guess we're talking about bosses, so if I have to pick one it'll be Morpheel! Mostly 'cause you battle him under water.
The bosses in TP were awesome, I really liked Stallord because it wasn't a regularly paced battle, and Argorok just looked fantastic (though he could be frustrating) but i'm gonna have to say Armogohma because i will never tire of swinging the rod and dropping a very heavy stone arm of justice down onto the creepy little blighter, and the little sequence after the battle was really nice, good place for some much needed humour =]