I voted Forest, Spirit and Ganon's Tower as my favourites.
Forest Temple is because the atmosphere was so good, it didn't stray from the theme but it also didn't get boring. That's a popular dungeon so I won't go into the choice that might because well it's all been said a zillion times.
Now, I picked Spirit because we have never seen that theme before or since. It looks as if it had remnants of the Light Temple, and maybe they could've made it more challenging or better than general, but I've always loved that dungeon because it's so beautiful, the music is great, and I like the fact it feels different to all the others, with a clear cultural input from the Gerudos. I think they could definitely work on the spirit theme a lot in future Zelda games, as it has quite a wide breadth as to what spirit even means and why it's represented and how.
I also picked Ganon's Tower because I liked that it had a little challenge relating to each of the themes, including Light. I know most final dungeons are like that in Zelda, and again it could be more difficult than it is, but even so, I thought it was a nice build up to the final battle, as well as actually showing to some degree what the point of the Sages really was, which is never clarified enough in the game in my opinion, because we see them first create the bridge to the tower and then breaking the spell on the inner tower enabling us to go up to Ganondorf for the confrontation. I think that's pretty powerful and an awesome way to begin the real end to the game
