Temple of Time because you traveled back in time... and I had fun playing with the statues. I loved chasing the stupid little spiders around, and made it my mission to kill every one of them... *muahahahaha*
It was also one of the only boss battles I enjoyed. I don't remember much of the others, hated Blizzeta.... I also liked the City in the Sky boss, but didn't like the city itself.
Arbiter's Grounds, Snowpeak Ruins, the goron Mines, The Lakebed Temple and the Temple of Time were all really enjoyable.
The Goron Mines was so innovative with their puzzles. The Lakebed Temple's design was also so interesting and complicated at the same time. I often got lost in that thing. Abriter's Grounds has such a good ambience to it and revived the Poe sisters in a way that went very well with this temple. The Snowpeak Ruins was completely unique has it was a ruined house. Plus, it included my favorite item, the Ball and Chain. The Temple of Time had such a great atmosphere to it and a great puzzle as well. The boss was largerly dissapointing, but I still liked it.
In the end, I voted for the Snowpeak Ruins, because of its unique puzzles, setting and item.
Looking over this list i realize how much I actually disliked the dungeons of this game :/ I did however like a few
I chose Arbiter's grounds. While the item obtained was very seldom used after the dungeon, I enjoyed the boss, the atmosphere, and I love how it reutilized the dungeon style of the OoT forest temple where you have to find and kill all four of the ghost things, except TP used the wolf senses to creatively enhance this
I hated Arbiters Grounds. When I was looking for the Poes, I was as Wolf Link. I used my senses to track them down. I then used first-person perspective. I turned around and saw a Stalfos behind me, which scared me. That happened almost all the time, and it was also as normal Link. Then there were the ReDeads, which didn't make it any better. But the Spinner and the puzzles were the only things that I liked about that dungeon.
My favorite would be the Temple of Time because it was really cool to use the Dominion Rod to control statues to kill any monsters. The mini boss was a fun fight. I had no idea on how to defeat the second half of it, so I was using every tecnique I learned up to that point.