Of the whole franchise, of course.
Mine could be Bongo Bongo(massive, bizarre), Dark Link(difficult and evil) Puppet Ganon from WW(great fun) and Twinmold(m a s s i v e, again.)
I would elaborate but I just woke up and I'm slacky.
What are yours?
1) Ganon (The Wind Waker) - It's fun, and c'mon, the little cartoonish Link impaling Ganon in the head's awesome.
2) Flying Dinous (Twilight Princess) - It's fun, pure and simple.
I just beat Uncle Rupee from Freshly Picked Tingle's Rosy Rupeeland yesterday. I wouldn't say it's my favourite boss but it is the most bizarre in my opinion. I mean c'mon, you fight cats!
I'd have to say Dark Link would be my favorite. Either that or Dodongo (The fight from OoT).
Ganon (OoT) - Come on, it's friggin epic. You can't tell me your mouth didn't drop when he emerged from the ruins of the tower and grew into the super-huge demonic pic.
Ganondorf (TWW) - Really easy, but the atmosphere of the whole fight was amazing, and the swordfight even still blows TP's final swordfight out of the water.
Stallord (TP) - This was just fun, with the Spinner and bouncing all over the place. Too bad the Spinner wasn't used more in the game.
Goht (MM) - Racing a giant mechanical goat as a Goron and slamming into it at ridiculous speed = amazingly fun.
I know there are more, but it's after 4AM and I can't think right now. XD
Plus this kinda goes into an idea of a feature article I had for the site, so...
I can't really decide. There's lots of bosses that look cool, but they can all be beaten easily. TWW and TP get points because the wait period between your attack opportunities is longer.
I do like Volvagia, Goht, Jalhalla, and Stallord. And Gohma from OoT just because I can beat her in six seconds. XD
1.) Evil Spirit From Beyond Phantom Ganon (OoT) A very interesting and fun boss in the way it foreshadows the final battle.
2.) Puppet Ganon (TWW) One of the most unique and challenging bosses.
3.) Vaati (TMC) The toughest Zelda boss I ever had to face.