1. Shadow Temple - I loved the whole scary atmosphere of the temple, with all the ReDeads, Wallmasters, Floormasters, and spiked walls and floors. I also loved the dungeon boss, Bongo Bongo. He was a very fun fight. Traveling through the temple was an awesome experience, and I was on the edge of my couch the whole time, anticipating danger at every turn. That's what I like from a dungeon. It might even be my favorite dungeon out of all Zelda games.
2.Spirit Temple - One of the main reasons I liked the Spirit Temple was because it seemed as if it was two seperate Temples, because you had to go through as a child and as an adult. The puzzles were very unique, and I liked how you had to go outside to get the Mirror Shield. This temple had what was probably the best boss and miniboss in the whole game. The Iron Knuckle fight was beyond epic, I loved it very much. And the Twinrova fight was also great, as it was a very fun, epic fight, while also being humorous, like when Koume and Kotake die, and are in shock that they both had halos on their heads, haha.
3.Water Temple - This temple gets a lot of criticism for being long, boring, difficult, and many other things. I myself found it very entertaining. I liked the challenge. The puzzles were very unique, with different levels of water raising and such. One of the main highlights of this dungeon was Dark Link. Dark Link was quite an epic fight, it was almost like you were fighting yourself. You had to use strategy in that battle, which is unlike most other minibosses and bosses. The boss, Morpha, wasn't as fun as I would've liked. It was a pretty basic fight and not very entertaining. But other than that, this temple was awesome.
4. (tie) Forest Temple - This temple, like most in this game, is very unique, but this one really stands out. You can go through many different terrains and can also alter the structure of the dungeon. Also, how about the music in this dungeon? I loved it, the whole eerie feeling to it. Although in this dungeon I didn't really like the miniboss(es) or boss. The Stalfos were okay, they're always fun, but the Poe Sisters, not so much. They were no fun and were just kind of annoying. Phantom Gannon is more of the same. He was a frustrating boss at first and is pretty boring, although I do admit I like how the battle set up, a room with 6 (I think it was 6, maybe it was 5) photos and the boss jumping in and out of them.
4. (tie) Fire Temple - I find this temple to be kind of the opposite of the Forest Temple in the sense of how good the dungeon puzzles were and the mini boss and boss were. I did not like the puzzles in this dungeon, I will have to admit. They were pretty boring and a lot of them were a nuisance. Some were better than others, but some were just kind of... Ugh. But The miniboss, Flare Dancer, is awesome. It was unique in how there was the furnace in the middle of the room and the Flare Dancer jumped in and out of it, trying to hurt you. Volvagia was also really fun. This is mainly because to me, using the Megaton Hammer is fun in general. It's kind of like those games at an arcade, Wack-a-Mole, or whatever they are called, where you have to use the hammer to wack the moles that pop out of the holes as fast as you can. I love how they implemented that into a Boss fight in a Zelda Game.
Don't let it deceive you that I put the Forest and Fire Temple at the bottom. I loved playing through all of these Temples. OoT had great dungeons, unlike many other Zelda Games.