My favourite is the mining facility or ancient cistern, the puzzles were imaginative and the ancient cistern boss was my favourite. Did not like Skyview temple at all though. I thought it was an appalling dungeon and I did not enjoy it at all. The boss was fabulous though.
Ill make a list of favourite dungeons in order like others have done.
1 ancient cistern- nice looking place, and the contrast of the undead area was great, glad to see the zomboblins are using the OOT ReDead tactic of jumping on your back and umm... Great boss, my favourite in the entire franchise, epic boss music and great fun
2 Lanayru mining facility- nice past music with well thought out and challenging puzzles, beautiful scenery during the minecart ride at the end.
3 Earth temple- good theme, fun ball rolling basically everything needed to take my mind of that horrible first dungeon
4 Fire Sanctuary- boring music but pretty area design, jumping into the mouth of the statue was fun and the puzzles were enjoyable
5 Sand Ship- Music really did not get me going, miniboss was not very fun, end of dungeon was great when the place flooded and the ship was split in two, but Tentalus despite being an ok boss looked like a monsters inc character and out of place, not scary at all.
6 Sky Keep- I did not like the room moving aspect, not fun at all backtracking, reused dungeon aspects, no boss, had to fight a miniboss like Scervo from Sand ship again who I disliked.
7 Skyview temple- music did not excite me, level design was uninteresting, just a bland and boring place, even the boss did not quite make up for the horrible place.