Eagle’s Tower from Link's Awakening is my favorite. It's open-ended and nonlinear in a way that few other dungeons in the series are. And the central puzzle is a large-scale dungeon wide affair, rather than a key hunt. If I had a criticism of it, it's that it doesn't offer very interesting combat.

My least favorite dungeon is from the Oracle games. I actually can't remember a specific one that I dislike the most, because the early dungeons in those games are so uninspired and without character that they blur together in my mind.