Favorite: The Earth Temple (WW). It's funny, because it used to scare the heck outta me when I was a kid, but now that I'm older, I really appreciate its creepy atmosphere. The floormasters are annoying at first when you don't know how to deal with them, but after you do? Genuinely a fun experience. I suppose pushing and pulling the mirrors in the mirror room is a little tedious, but solving the room gives me enough of a dopamine hit that I don't really mind it too much.
The Palace of Winds from Minish Cap is a close second, the puzzles and even the platforming are actually pretty fun, and the music is a bop. The boss fight against the Gyorg Pair is also neat.
Snowpeak Ruins from TP gets third-- I like the design and the concept-- an abandoned winter retreat/fortress that's now home to friendly yetis? Yes! I love how it's basically just a house, but a really cool (pun intended) one! And it's overall pretty fun, but the ice physics are why it's third. Also the yetis are adorable and I love them.
On the flip side...Coming in at number three for my least favorites it's... the Forsaken Fortress! Considering how many times I've played Wind Waker, I can safely say that this is my least favorite dungeon in the game-- and it's mostly the second go around that I really dislike, as I dislike replaying dungeons in a single run of a game in general. Still, it has the first Phantom Ganon fight in WW, you get to smash the Helmaroc King with a hammer, and I do like the first go around (stealth segments and all), which is why it's only third.
Second least favorite is every Divine Beast (save the DLC one which feels more like a proper dungeon) because they just aren't really dungeons? They're fun enough for what they are, but they just feel... lacking. (TotK handled dungeons much better, in my opinion-- yeah, they were still kind of short, but they actually felt like dungeons.) I don't play BotW or TotK for the dungeons, though-- I play 'em for the overworld exploration. That's what keeps the Divine Beasts at second.
And my least favorite dungeon is The Temple of the Ocean King. Because, as I stated previously, I really hate having to retread through dungeons in a single playthrough of a game. And hoo boy, is it repetitive. Yes, you can unlock shortcuts. It still doesn't help the tedium. It's why, despite enjoying the rest of Phantom Hourglass immensely, I've never replayed it. (Edit: It's also on a timer. Apparently I hated that part enough that I blocked it from my memory).