Although it is considered the hardest dungeon in Ocarina of Time, I like the Water Temple. It is indeed confusing and it is difficult, but I'm always up for the challenge.
Forest Temple is pretty much straight forward favorite Zelda dungeon for me, because you get an awesome weapon called Fairy Bow and play game of tennis against Phantom Ganon.
The Water Temple is definitely my favorite. It's not very linear because of how the keys are placed throughout the dungeon, and it's the only main dungeon in Ocarina of Time in which you can finish with an extra key without glitches. I've played through it many times while collecting different keys and collecting the keys in different orders. This dungeon has excellent replay value and figuring out the optimal path through takes some real thought.
For instance virtually every guide has you change the water level five times when you can actually beat it with only three changes by skipping a key. Also for instance I like to grab the key people typically get second (in the whirlpool) as my fifth and final key out of the six in the dungeon.
I didn't even have to think about my answer. Shadow Temple.
I absolutely love the dark atmosphere in that entire dungeon. On my first play through, I was both terrified and fascinated by the design (with the skulls and undead and everything) and the voices that would call out to you. Plus, in my opinion, the Lens of Truth is one of the coolest items in the series. Finding secrets with the Lens has always been a favorite of mine; it's too bad that I now know them all and the factor of surprise and subsequent satisfaction has worn off. Oh, and don't get me started on the music in this temple. It's incredible and fitting and... creepy.
The Shadow Temple has and always will be one of my favorite Zelda dungeons of all time. None of the other undead-themed dungeons in the series have really had the same effect on me as this one did.
I love the forest temple, because to me it is the perfect dungeon. It is creepy, challenging, fun, and the boss is just so much fun to fight. When I was little this dungeon scared the hell out of me and made me stop playing for a while, because I was afraid to look for the Poes lol