(Note: I speak freely about the contents of each temple, so if you are worried about being spoiled, you shouldn't read the discussion portion.)
I tried to think of a bottom five, but only four really came to mind. And of the four, the only temple that I actually dislike is the last one. This also doesn't take into account the many Legend of Zelda games that I haven't played.
4. Woodfall Temple (Majora's Mask)
I hesitate to even include this because it wasn't really that bad. I want to give it a pass for being the first dungeon. But the thing is, Majora's Mask only has four dungeons. So you can't really give any of them a free pass just for being the first. Especially when the others were all so great! Snowhead had the giant tower room/pillar, Great Bay had the pipes and water directions and the fire and ice arrow puzzles, and the Stone Tower temple of course could be flipped upside down. So what is special about Woodfall? Well, for one... it smells bad. Also, there's... a giant wooden flower that spins? I think I would probably not be as critical of this temple if it weren't for how few there were in the game.
In its defense, I think the swamp/jungle theme carried well throughout. I just wish that it had been more expansive or more difficult, because it accounts for 25% of the game's temples...
3. Fire Sanctuary (Skyward Sword)
This dungeon really bugged me for some reason. After the Lanayru Mining Facility, Ancient Cistern, and the Sandship, all of which were very fun and interesting, there was this dungeon. Unlike the prior two, which developed the themes of their respective provinces in the second set of dungeons, Fire Sanctuary seemed pretty lame. I mean, did the game really need two fire temples? The dungeon item was... actually I can't remember what it even was. Let me look it up.
Oh right... the Mogma Mitts! They remind me unfavorable of the Spinner from Twilight Princess in that they are only useful in very specific locations, and are otherwise useless. I really think these could have been combined with the Digging Mitts into just one item that did both things from the first time you got it and add something more interesting for this dungeon. Finally, the boss was a retread of the first boss. I was expecting, actually, an early ancestor of Volvagia to be the boss, which is why I was so disappointed that it was just a Ghirahim battle. At the very least, they could have had a Ghirahim fight followed by him getting so angry about his defeat that he summoned some sort of boss creature afterwards.
So the main reason I didn't like this temple is that it felt extra in almost every respect - there was another fire temple, there was another mitt item, and there was another Ghirahim battle. This leaves the contribution of this temple to the game at:
• Frog Tongue switches
• Water Fruit
• Angry Centipedes
I'll just leave it at that.
2. Spirit Temple (Master Quest)
Before you get all mad at me for hating the Spirit Temple, I actually love the original Spirit Temple! The Master Quest Spirit Temple, on the other hand... is a disaster. I didn't completely hate this temple, because I did love the challenge of it. However, some of the puzzles were very poorly thought out. I'm thinking mostly of the room that has three time blocks in it, where you have to play the Song of Time in a specific order in different places in order to make a crate fall into place without disappearing into a bottomless pit. Having to play the same song over and over again to try and solve this picky puzzle was very irritating for me. I also feel that this temple was poorly designed because it required many more trips back and forth through time to get all the Golden Skulltulas... I'm pretty sure in the original that if you know where stuff is already, you can do it with only one trip to the child timeline. Plus, the water on the right hand side when you enter felt really out of place in the middle of a desert. What insane Gerudo architect of the past would design a building that wastes so much water when you could just block it off with a rock or something?
1. City in the Sky (Twilight Princess)
The boss battle, while kind of fun, is not enough to save this from being my least favorite Zelda dungeon/temple that I have come across. When I first arrived in the area, I was excited to see what was going to be up in the sky. Unfortunately, it was... this. As BeastModeMan97 mentioned above, I too returned to the main room without activating the switch on the ceiling. And then, as a result, I had to backtrack through the entire temple again. The whole weird-sounding-Oocca-noises-as-a-song thing was cute for about five minutes, but after that I was getting very annoyed with it. The dungeon item was a huge disappointment - while I like the double clawshot in practice, I feel like we should have gotten two of them off the bat like in Skyward Sword. It felt like the developers couldn't think of a unique sky-based item so they just went "we'll just add... another clawshot!" This dungeon was such a disappointment to me because overall, I really enjoyed Twilight Princess's dungeons. I even liked the Snowpeak Ruins, though it took me a while to realize that it actually was a dungeon...
Honorable Mention: Temple of Light (Ocarina of Time)
This always annoyed me for not actually being a dungeon. I imagine a place with a bunch of mirror/prism/lens puzzles, but they sort of put that in the Spirit Temple instead.
