The Forsaken Fortress in Wind Waker. It didn't really feel like a dungeon to me. Especially the first time going through it because it's primary focus was on stealth. I generally don't enjoy the waiting around involved in stealth and I ended being sent back to my jail cell and having to start over again several times. Plus I didn't like that my sword was missing and rather than getting a cool new dungeon item, the focus was trying to find the item that I lost.
TP's City in the Sky. While I love the theme of a city being in the sky, and the thought of Hylians living in the sky is a great set-up for Skyward Sword, this temple felt just... bad. It was boring and tedious having to trek through it. The music is straight up annoying. The overall design didn't seem to fit the concept as well as I would've hoped.
Simply put, this temple felt more like a chore than a challenge.
Anyway, I'll say here what I said wherever I said it. The worst dungeon, in my opinion, is Inside Jabu-Jabu's Belly. This dungeon disgusts me and I dread the thought of reaching it. I really don't like the premise for it and it's not even a fun dungeon anyway. The enemies are simply annoying, the layout is repetetive and the way everythign pulsates and wriggles turns my stomach.
I really, really do not appreciate being made to de-worm a giant fish.
Favorite: I love Lakebed Temple, Snowpeak Ruins, Temple of Time and City in the Sky! (obviously someone likes Twilight Princess...) Oh, and the Fire Sanctuary too.
Least Favorite: I always feel uncomfortable going back to the Forest Temple from TP, and actually also partially the Ancient Cistern.
Well, a thread merge... Time for me to give a new answer!
My favorite is probably a tie between the Sandship and Stone Tower Temple. They're both overall fantastic dungeons that I look forward to playing through more than any other in the series.
My least favorite is beyond the shadow of a doubt a tie between the Wind Temple and City in the Sky. Both of these dungeons are irritating beyond belief by presenting puzzles that either, rather than pose a challenge, slow you down or situations that are difficult to overcome strictly due to frustrating and confusing design rather than something that takes effort to overcome.