My favorite dungeon out of all Zelda games is the Water Temple of Ocarina of Time because of how open-ended it is, and I liked how most of the keys were hidden. I especially liked how changing the water level opened up different parts of the dungeon. Two of my other favorite dungeons also contain a global puzzle mechanic as well- Stone Tower Temple and the Sand Ship. Stone Tower Temple is awesome because of how well different items and masks are incorporated into the gameplay of the dungeon, and the flipping mechanic leads to some really hidden stray fairies. The Sand Ship was awesome because of the timeshift mechanic which greatly affected how you could access rooms, and it also was fairly open-ended.
My least favorite dungeon might be the Goron Mines of Twilight Princess. It's not a bad dungeon, and I don't hate it. However, there were a few things that bothered me, and those elements are enough for me to not like it as much as other Zelda dungeons. First off, I really thought the iron boots' usage was clever, but in practice walking at a fraction of normal speed became really annoying really quickly for me. I thought it was especially sadistic to make you walk on the magnets even more if you want a heart piece that's not even hidden that well anyway. Secondly, the idea of breaking a boss key into pieces is great, but it was pretty pointless in this dungeon because of how linear it was. It's not bad, but IMO it's just a waste of a good idea by putting it in the wrong context. Finally the boss of the dungeon is probably my least favorite of Twilight Princess, and I thought it was a fairly forgettable fight.