I'd have to say either Bongo Bongo or Twinrova. It's hard to choose between the two. Both were excellent bosses for the two best temples, in my opinion, in the game. Twinrova was great in that you had to actually use your equipment to defeat them. I don't mean equipment as in the weapons such as the boomerang, slingshot, and all that, but as in something you can equip such as the boots, sword, and shield. The Mirror Shield was a fantastic item, and they gave it a fantastic use in this battle. I always got a kick out the scene where they were dying and having a fit, too.
Bongo Bongo was great because I loved the whole dark spirit thing he had going on. The bodyless hands and eye(until you used the lens of truth) was really awesome. It was pretty unique how they put the drum in there and had him banging on that thing, too. He uses one of the other great items in the game, the Lens of Truth. The Lens of Truth was a pretty awesome item and had a very good use, and I love how they made him mostly invisible here. It gave the battle a whole new feel, in my opinion.
Overall I suppose I'd have to go with Twinrova, though. Mainly because of the fact that they are more closely related to Ganondorf, being his surrogate mothers.
i just started the game few days ago 
so Ive only got through first boss but i will say that IT was pretty easy for the first boss so the only one i can pick atm is The first boss! hehe 
