I played only all the games from LttP, i can't really remember what the Dungeons from Links Awakening are.
LttP: Death Mountain
Well, it was the last Dungeon from LttP before Ganon's Tower. Also i don't remember much about this Dungeon, but i have always said this one was my favorite from LttP. I must start over the game some time, only it looks difficult for me now. Don't ask me why but died to fast and much. Fail.
LA: ?
This game is really hard to remember. I don't even know the name of the Dungeon, but is was a kind of water Dungeon. You could dive under water and i can be wrong, but there where keys on the bottom of the water.
OOT: Shadow Temple
I played this game over and over again and the Shadow Temple stay my favorite, i like the Dark things around, undead enemies. The room with the guilliotine was just amazing. The big drummer Bongo Bongo was a great challenge too, now he is so easy, while i had trouble with beat him in the past. I like it if he drums, so much fun, and his hands are sometimes too... fast... xD
MM: Stone Tower Temple
In the beginning i looked at this one and had only one though. ''This Temple is too diffcult for me'' First i played this one with cheats, Nepolink is such a cheater, after it i wanted to play it without cheats and walkthroughs. (well i only used the 'Press L To Levitate'' Cheat) The harderst part was the treasure chest in the beginning, i walked around and around over again after i finally figured out about that chest. But the Stone Tower Temple is the best Dungeon i ever played, and by this it's my favorite all over the Zelda games. Only one this, i hate Twinmold, it's too annoying.
WW: Tower of The Gods
I really love the Earth Temple, because it's one of the Dark Temples, i love Dark Dungeons. The ''Purple Gas'' something that gives you a reverse control was amazing. But Tower of the Gods was more spectacular. I love the structure and the command song. Gohdan was one big bomb of fun to beat, but also reminds me of Bongo Bongo. The world beneath Tower of The Gods was great, i love Ganon's Tower too.
TP: Arbiters Grounds
The same as above, i have a weak spot for Dark Dungeons like this. I totally love the old Tomb idea. Arbiters Grounds knows only one kind of enemies and that where the creepies ones. I remember the room with the torches, if you burn the wrong one MANY skeletons raise from the sands, scary.
I was stuck with the mini-boss the Death Sword. I used Link only i his normal form while i needed the Wolf. xD Stallord was also a great boss, i lvoe it's second battle.
PH: Ghost Ship
Well, the Temple of the Ocean King was also nice, but the Ghost Shop had the most difficult puzzle, then i look at the one with the levers about the drums. The ''Shinigami'' like Phantoms are the greatest of whole PH. But the Kubus Girls where creepy, I knew already that they are evil or something with the Final Boss. That girl who said ''choose the left'' was the biggest example, i didn't open the left one though. xD
FS: Death Mountain
The song of this mountain was just epic. I didn't play FS many times, i only played it on a emulator because the lack of people. Me and my brother controlled 2 links each, we did beat the bosses and the whole game after all. Death Mountain was my favorite, especially the boss.
Unfortunate i don't have FSA. :c
Edit:
I forgot about MC
MC: Palace of the Winds.
I really love to jump around with the Roc's Cape. It was like City in The Sky from TP. Oke, i got stuck on some places but that makes the Dungeon a good challenge. The music was so nice, one of the best Zelda tune i even heard.