Not sure about my order of these, but some thoughts from games I've played. I find myself favoring atmosphere and gameplay the most, complemented by music. I may do a least favorite list tomorrow.
Best
Palace of Darkness (ALTTP) - First dungeon to greet you into the Dark World, that great dungeon theme, and the overall atmosphere gearing you up for the much less light-hearted Dark World dungeons. Helmasaur was a pretty challenging boss too.
Face Shrine (LA) - Even better if you include the Southern Shrine, which introduced the most existentially eerie sequence of this game culminating in a big hint that the game, and Link's existence as a whole, was not real. The music really makes this section too. The main dungeon is one of the more difficult but also more fun dungeons in this game. Honorable mention to Catfish's Maw.
Spirit Temple (OoT) - The atmosphere here is incredible, as you feel totally immersed in the remote environment to even reach the dungeon, and then as you explore the cavernous depths of the dungeon itself. It's hard not to picture yourself as young Link, see a passageway only accessible as adult Link, and imagine how the dungeon would have aged during the seven year absence as you explore the second half. The Iron Knuckle represents one of the best swordplay fights of the game, and the echoing music makes the dungeon seem like a relic through which you must deftly navigate prior to your final battle.
Stone Tower Temple (MM) - Most things have already been said, but what a creative mechanic to cap off a complex and rewarding journey. The boss battle is a clunker, but that doesn't matter much by the time you get there.
Temple of Time (TP) - I've seen differing opinions on this one, but I fall firmly in the "love it" camp. Sort of Spirit Temple-esque, it presents you with a set of puzzles, then switches the gameplay mechanic halfway through, making you rethink your entire approach and somehow force you to innovate a new route doen a seemingly old path. Love the atmosphere.
Sandship (SS) - I love dungeons that seem like believable locations. This dungeon was a true-to-form den of puzzles, but also a totally believable pirate ship complete with a swordfight on a plank. Great use of the brilliant timeshift stone mechanic. Boss fight was sort of a clunker, but as with all others on my list, atmosphere took it a long way. Honorable mention to Ancient Cistern.