There are 4 major dungeons. I don't remember many of the mini dungeons, but places like the Pirates' Fortress could count. Which one was your favorite?
I haven't played in a while, but I did enjoy the Snowhead Temple. The boss was particularly fun. Like all other Zelda bosses, it was fairly straightforward, but this one was also more enjoyable at the same time. What can I say? I like chasing an evil bull as a spiky Goron. Dodging the bombs makes it even better. I don't remember much of the temple itself.
I as I have yet to play a Legend of Zelda game, I cannot say I have one. I really should go and buy Wind Waker so I can finish it (I borrowed from a friend) Also I really should play through the N64 ones.
My favorite dungeon is the one on the moon it was interecting and some things were challenging. I like it because of the fact you needed to defet every foe to get to the end to bad it was too stright forword.