Definitely the Wind Temple. The main room was just annoying to navigate by rising up with the fan. It was extremely difficult for me since I didn't have the extended magic meter at the time. Makar wasn't very helpful, and it was just annoying to have to rescue him when he got kidnapped. Although the boss, Molgera, was a wonderful part of the dungeon. Probably the only good thing about it.
As for favorite, I'm going to have to go with Ganondorf's Tower. The dungeons in Wind Waker weren't as good as the ones in the other Zelda games.
Mine would have to be the tower of gods because it is just plain annoying and the Wind temple so hard navigating with that stupid fan i didnt have the extended meter and everything like that and makar was the worst part i hate having to be makar or medli.
My least favorite is Dragon Roost Mountain. When I got the Wind Waker this year I was really excited, but that dungeon was so boring that I felt like not doing it. But I did. All the other temples/dungeons were good.
I never really liked the first dungeon, mainly because it's like you could hardly do anything at the beginning. But once you get going, it's fun. I also never liked the ending part (the mirror room) in the Earth Temple.
My least favorite dungeons- though I'm not saying that I didn't like them, but I liked them the least- were probably the Dragon Roost one and the one where you saved the small deku scrub. I liked certain elements of those, especially the boss fight saving the Deku Scrub and climbing the side of the volcano in the Dragon Roost one, but all in all, they felt a bit... small and easy to be dungeon to me. Still liked them a good amount though.
Tower of the Gods. The name implies a sense of grandeur and elegance, yet I felt like I was walking through an alleyway the whole dungeon. Horrible design. I have to say though, most of the dungeons in the Wind Waker seemed like randomely generated instances rather than a carefully and lovingly prepared temple. It was as if they spent most of the development planning out the overworld and sidequests, then slapped together a bunch of connected rooms with some keys thrown about. I'm not saying it's a terrible game, I'm just saying that this particular end of it wasn't handled very well.
Well, the Dragon Roost Cavern dungeon was too easy, in my opinion. But it was the first dungeon, so it would make sense for it to be easy. So I have to say the Wind Temple. Makar was a real pain and such.