Hmm, I guess I'll just say my favorite/least favorite from the games that I have played.
Ocarina of Time (Favorite): The Forest Temple. I love the creepy atmosphere, strange puzzles (like the twisted hallways... whenever I think too hard about how gravity works in this temple, I just get confused). The music is one of my favorites from the entire game, and I love poes, so having a ghost-themed dungeon was fun. Even the boss battle is good. I found it challenging but not overly so.
Ocarina of Time (Least Favorite): Bottom of the Well. I actually do enjoy the creepy aesthetic here, but several things bother me about this place. First, unless you're going for the Golden Skulltulas, you aren't forced to enter more than two rooms in the entire dungeon, making most of it kind of pointless. Second... it really bothers me that all of these corpses and pools of toxic goo are being stored in Kakariko's water supply. Doesn't anyone in the town wonder why the water smells/tastes horrible?
Master Quest (Favorite): Inside Lord Jabu Jabu's Belly - I thought the original was a weird dungeon, but Master Quest makes it even more bizarre. I was so surprised to find cows, and even more surprised to find that the cows were actually switches. I liked that carrying around Ruto was minimized, and overall the dungeon was very fun and weird compared to the original, which is weird but not really that fun.
Master Quest (Least Favorite): The Spirit Temple. After finishing the Shadow Temple without too much trouble, I was ready to breeze through the Spirit Temple... It was agonizing. The time block puzzles are honestly obnoxious. It took me about 8-9 tries to get that stupid crate not to fall into the abyss, and it took me about forty-five minutes to find a certain eye switch...
Majora's Mask (Favorite): Great Bay Temple - I found this temple to be a great balance of difficulty and fun. I enjoyed tracing the pipes to their sources, the various Ice Arrow puzzles, and some of the stray fairies are challenging to obtain. Though this temple is confusing, I thought it had challenging but ultimately intuitive puzzles, and reversing the current was a fun twist.
Majora's Mask (Least Favorite): Woodfall Temple - To be fair, Majora's Mask only has four dungeons. And I feel that though there were so few, each one is well-designed. Woodfall is just the least compelling to me, compared to the other three. The mini-boss battles were bland (Gekko was okay though). The item, though important, was nothing surprising or special. It's also much shorter than the other three. I think it was pretty good in its role as the first dungeon, but I don't think any of the other three deserves the title of "worst".
Twilight Princess (Favorite): Lakebed Temple - From the creepy music, the waterwheel/stair puzzles, to the hilarious miniboss, this temple was definitely my favorite. I loved the difficulty level which was high enough to keep my attention but low enough that I didn't rage quit.
Twilight Princess (Least Favorite): City in the Sky - I don't even really want to talk about this one. 90% of the ground is an abyss, the music is basically freaky Oocoo sounds, the item is a disappointing repeat, and the aesthetic is very light but without much contrast. The one bright spot was the boss, but by the time I got there I just wanted it to be over.
I haven't finished Skyward Sword yet, so I'm not sure how many more dungeons there are. My favorite so far is the Lanayru Mining Facility, while the Fire Sanctuary is the worst.
