The Water Temple from OoT was challenging, but I will have to go with the first dungeon from AoL. I am not sure about any of the others from AoL because I haven't beaten the first and don't intend to.
I agree with Random Person. I recently picked the game (AoL) up on the 3DS Virtual console and cannot pass the first dungeon even while using ZD's walkthrough.
1.-King Dodongo-OoT
2.-Scaldera-SS
3.-Stallord-Tp
4.-Ghirahim round 3-SS (it's awesome when you do the fatal blow on him when he falls off the edge)
5.-Koloktos-SS
6.-Demise-SS
7.-Tentalus-SS
8.-Argorok-Tp
9.Phantom Ganon-OoT
10.-Fyrus-Tp
The bosses don't get much harder as you go through the game...... at least the first 7 are pretty easy (in palace of twilight now so haven't fought last two)