Yeah, I'd have to agree with TeaVag, but I think any place with floor masters is tough.
Although Shadow Temple still holds the record for the longest time of all dungeons for me.
In Wind Waker, hmm....It wasn't hard, but it was the most fun part in the game, when you pull the master sword and all of the enemies, hoards of them come back to life and you have to kill them, best part ever. Very tactical part too.