swamp dungeon in LTTP.

I just finished the Tower of the Gods in Wind Waker a couple of days ago. It was pretty awesome. I haven't gotten to it yet but I recall the dungeon where Link and Makar team up was pretty impressive. I'll hold my comments until I finish this replay.

I think Twilight Princess is Zelda's finest hour, but none of the dungeons are jumping out at me. I need to replay this one too!

Hm, actually I found that temple very enjoyable.  Having to return there and descend a bit deeper each time was never a chore for me; I liked the countdown as well, trying to find (and annotate on your map) the ideal path through the temple with the highest possible number of seconds left on the clock.  Trying to get past all the guards in record time was also great practice for the multiplayer force-gem game.

the desert temple in TP
and, the Shadow Colossus in OoT

for some reason both deserts in those two games just grab me. I love gerudo valley and the shadow colossus, them put together is just an awesome experience. I also love the final battle in the desert temple in TP (with the spinner + gaint column)

Shadow Temple by a longshot.

OOTs water temple was easy, the only hard part was that hole under the rising platform.

my favorite would be the stone temple in majoras mask, with all the ocultist and sexual imagery in it, it was actually disturbing reading all the theories about it.

I personally thought the Temple of Time in TP was cool and the Well in OOT, scary at first but once you figured out where everything is it got alot easier.

Water temples in OoT, MM and TP, ice temple and the rockvale temple in MM and desert temple in OoT. I

This includes the Desert Temple with the spinner... so I will denounce your opinion right here and now.

I've only played the console Zelda's after LTTP but everyone has one or more favourites

LTTP: Ice temple. The desert temple here with the holes was also amusing.

Ocarina: Forest temple and Desert temple (awesome music)

Majora's Mask: Water and Stone. Though I greatly enjoyed the Bull-boss

Wind Waker: Tower of the Gods.

Twilight princess: Desert temple and Sky city (double clawshot woehoe!)

Since you mentioned it, the spinner was the most disappointing item in TP.