Probably Zant. It's such an anticlimax, it rocks. He reminds me of Kefka from FF6, in a good way.
Diababa, Fyrus and Morpheel were all pretty cool, but way too easy.
Stallord was great, but I didn't like his floating head part. How about using the spinner to "spin" up his bones and ribcage, a bit more like SotC.
Blizzeta was "cool" too. Some more difficulty would've been nice, but the cutscene with Yeto and Yeta after the fight make up for it. <3
Armoghoma was awesome. Just too easy. But seriously, squashing that fat spider with statue hammers... and then the 2nd part with the little spiders. Priceless
Argorok was very nice. Epic, and not too easy, but the Peahats didn't really fit in.
Ganon rocked in all of his forms.
Some very nice concepts behind all of the bosses, but they're really too easy.