Ancient Cistern by far.
Some of the best Zelda dungeons are the places that transcend the walls holding the labyrinth together. There's a distinct feeling, a texture and a history that speaks volumes on what transpires in the dungeon. For the Ancient Cistern there was an atmosphere given off by contrast produced form positioning the warm, heavenly regions above the sinister (and frankly, unexpected) caverns below. It was an architects depiction of heaven and hell, life and death, and the imagery was unforgettable.
On a more technical note, the dungeon was incredibly smooth in terms of game play. Each puzzle rolled off the next without being straightforward or creating a "domino effect", while enemies and boss fights never stood out of place and added a more cinematic feel to the whole crawl. It also ensured that the play would be able to gain proficiency with the whip by presenting a multitude of challenges that the item could over come (swinging over a gap, turning a leaver, ripping components off the body of Koloktos, etc.) an still ensured that the rest of the inventory would have a part to play.
This dungeon is a testament to the power of a Zelda game, bereft of the clunky modern story telling mechanics found in games today, as well as a shining example of what can happen when a few design geniuses blend art, innovation and story into an interactive medium.
P.S. I like Zelda way too much. :chu: