One boss fight I remember liking a lot was Onox's dragon form in Oracle of Seasons, I mean, apart from it looking awesome and finishing an already pretty much perfect game, it was just a fun fight. Not too difficult, yet more than difficult enough. The fight with Onox himself wasn't all that bad either.
But other than that, Mothula. I mean, in OoS, that thing is too cute for words, and in AlttP, it's one hectically awesome bossfight (and oddly enough the most memorable as well, apart from maybe Ganon).
Though he's not a boss there, (only a mini-boss, and a simple enemy after that), the Wind Waker version is by far the most awesome (and was actually the inspiration for my Firefox skin).
The fights with Ganon(dorf) are still amongst the most fun and challenging boss fights, though, and always seem to end the games perfectly. Puppet Ganon from WW and Possessed Zelda from TP are probably my favorite versions, the 1st for being the most ridiculously hilarious final boss in any video game, ever, I don't think I ever laughed as hard at a boss in my life, especially since I was expecting something far more threatening. And the 2nd because, well, it's Zelda, floating around, trying to kill you, no further comments required.
Honorable mention goes to Dodongo for disliking smoke, being the very 1st boss, ever, and inspiring a legion of enemies and other bosses. Also, Jalhalla (the poe overlord from WW) for having the most awesome background music (as far as I can remember).