Some of my personal favorites were:
Stone Tower Temple: a nice culmination of all you have learned through the game, good puzzles and excellent music. The only real downside was the boss...
Spirit Temple: Clever use of the Mirror Shield, liked that it had both a young and adult section. Decent music, good mini-bosses and a great boss.
Sandship: I liked the whole time manipulation aspect of the Lanayru dungeons, and the Sandship was where it was best used. An excellent mini-boss and a good boss.
I'll keep it limited to top 3, or I'll be here all night...
Stone Tower Temple: a nice culmination of all you have learned through the game, good puzzles and excellent music. The only real downside was the boss...
Spirit Temple: Clever use of the Mirror Shield, liked that it had both a young and adult section. Decent music, good mini-bosses and a great boss.
Sandship: I liked the whole time manipulation aspect of the Lanayru dungeons, and the Sandship was where it was best used. An excellent mini-boss and a good boss.
I'll keep it limited to top 3, or I'll be here all night...