How can there be a discussion about great Zelda dungeons that doesn't include the last temple from Zelda 2?
Seriously, it's not often one finds a dungeon that hates the player so much as that one does. First of all, even MAKING it to the temple is a feat in itself, trekking through troublesome ground and dodging annoying, slightly Link-relative flying enemies over pits of fire... And that's little more than a kind introduction to the dungeon itself. The branching paths and repeating rooms serve only to lead you astray (if not to a dead end) within this labyrinth of a last level, populated with merciless enemies found nowhere else. It is a dungeon where your survival depends upon your choice of paths, of fights, on your wise use of a dwindling reserve of magic (you never recover hearts from defeating enemies in this game, in case you don't know), and of remembering and exploiting all of the tricks and secrets that you'd learned from previous dungeons. It is a battle of endurance - a siege - of Link, armed with a few lives, a litany of moves and spells, and a single health bar, against the sprawling, inanimate foe that is the temple, all set to a foreboding tune that says "we mean business".
Suffice to say, it's one of my favorite Zelda dungeons to date.