For me it was definitely the Ancient Cistern. I appreciated the fact that it was original in that it was different from all the other water temples of the past Zelda games. I also liked the recurrent theme with the giant statue, the cursed bokoblns, and even the possessed automaton boss of the dungeon.
I completely agree about the Ancient Cistern. I love the contrast with the pure, sort of Buddhisty top layer with the polluted lower floors. The boss was mad and probably the best one in the game - took me much longer to defeat than the final boss! The whip is also my favourite weapon. I think this temple definitely wins!
Definitely the Ancient Cistern, it just has so much depth and meaning to it. Has anyone else read the article on zeldadungeon.net about this dungeon? It's based on Japanese a short story. I thought that was pretty interesting.
Definatley the Ancient Cistern. For ONCE a water themed dungeon isn't so frustrating like the Water Temple, Lakebed Temple, or Great Bay Temple. It was very enjoyable and the design was just amazing. Plus Koloktos was a very cool and fun boss to fight.
No question in my mind. Easily the Sandship. Don't get me wrong, I loved EVERY SINGLE one of the Dungeons in Skyward Sword, but Sandship was by far and a way the best. I really enjoyed it. I really liked the setting as it seemed to be a unique one. Also the backstory to the whole place was cool. Plus it was a very beautiful place in the past setting.