Spirit Temple of OoT at the top with a bullet. The ambience in there is unique, it gives it an Arabian touch, like you're inside a pharao's tomb or something... And of course you get to go there in both timelines, that rocks!
Second is Stone Towers from MM. REALLY big dungeon, and the timelimit of 72 hours (or minutes) isn't really helping. The Boss of this dungeon has een done very nice, I'd been wondering how the sandworms would look in 3d ever since I fought the 3 worms in AlttP, in the second dungeon.
Third would be the Earth Temple in WW. Way better use of mirrors than in the n64 games, and of course you get to control Medli, I love that girl...