My favorites would be Dragon's Roost, Tower of the Gods, and Forsaken Fortress #2.
My reasons are:
Dragon Roost: First dungeon of the game, It set things off at an epic pace, You had to think a bit to get past some rooms, Use water jugs to get across lava in places, And got the Most useful(if not the second) Item in the game. I used the grappling hook almost non-stop. (The whip in SS could've learned a thing or two)
Tower of the Gods: Only level you can bring your boat inside of. It was a big test of skills learned earlier in the game, plus added new skills-utilizing the command melody and archery. It introduced Darknuts. It also had plenty of optional areas to explore.
Forsaken Fortress#2: It starts off with you feeling epic from slaying an army of moblins and darknuts after drawing the Master Sword.
You then beat Phantom Ganon at Light Ball tennis. It ends in one of the most bittersweet moments in the game, You find out you still can't beat Ganon But you know your sister is safe (sorta) with the pirates.
These are my reasons for choosing the dungeons.