Choosing one dungeon from this game, is like choosing which child i would save in a fire! such a hard decision. All of the Dark World dungeons are equally great, Turtle Rock being the most frustrating but cool at the same time. The Thieves Hideout, can be tricky if you dont know the game like the back of your hand, making it a good challenge. But I decided to base my decision on pure enjoyment.
Playing through the first two dungeons of the game, you are just learning the ropes. Upon reaching the Tower of Hera, It's basically saying "Lets see what you have learned before we throw you too the wolves." At this point in the game, they are basically letting you know that, you cant just think about the room you are in when solving a puzzle. This dungeon is where they inform you that some puzzles will be spread out in multiple rooms to get to one solution. For example making sure the right colored blocks are raised, otherwise you get half way across the dungeon to figure out you have to go all the way back and hit a switch cuz some switch blocks are keeping you from progressing. They also introduce you to thinking vertical as well. Like to obtain the moon pearl for instance, not only do you have to go to a floor above, but you also have to make sure that the holes cause by the star tiles are in the right spot before falling from the top floor. Also depending on the size of the hole, and depending on which edge of the hole you fell, you would land in different spots. This blew my mind for an SNES game.
And for that my vote will go to the Tower of Hera, simply cuz the joy you get when you realize, that "If this is only the third dungeon, I'm in for some difficult times"