My favorite dungeon of all time is probably the Forest Temple from Ocarina of Time. First of all, at the time, it was beautiful, and the twisting corridor idea was absolutely awesome and really made it very fun. I think it was innovate and a difficult (but not annoying like the Water Temple -- which was perhaps equally as genius).
Man, looking back, it's clear that Ocarina of Time was an amazing game.
I also thought Phantom Ganondorf was much harder than the real Ganondorf (and Ganon).