LOZ: haven't played in a long time, but I know I hate the final dungeon.
LTTP: I greatly dislike the Skull dungeon and the one in the middle of the lake in the Dark World (No idea what their names are). I've only played the game one and a half times, so I don't really have a favorite yet.
OOT: Favorite is the Spirit Temple or Ganon's Tower. Least favorite is Bottom of the Well and Shadow Temple.
MM: I like them all, but Woodfall is least favorite. Favorite is probably Great Bay, actually.
WW: I dislike both of the sword dungeons. I like Forsaken fortress a lot, but actually my favorite part of the game is sailing around to all the islands and solving all the puzzles and such.
TP: Least favorite is definitely the Lakebed Temple. Favorite ... hmmm, I like all the others, but at the moment I am gonna say my favorite is Yeto's house.
MC: Oh wow it's been a while, but I don't like the mountain dungeon. And I love the Temple of Droplets.
PH: I like the Temple of the Ocean King, and the final "regular" dungeon, with the pyramids. I really don't like the earlier dungeons in the game, they are insultingly easy.
ST: Hmm... Hard to choose. I like the Tower, except the unlighted floors. Least favorite ... can't say. They are all kindof equal in my mind.