For me it's a close one. I really liked the Arbiter's Grounds in TP. It had a variety of puzzles since it was the first full dungeon you explore after you gain the ability to become a wolf at any time. The spinner added a nice element toward the end too. The boss battle was a bit more unique as well.
My favorite out of the list though has to be the Spirit Temple from OoT. Nice puzzles and the fact that you have to play it as both young Link and adult Link adds a nice element to it as well.