Design wise, Palace of Twilight + Hyrule Castle take my vote. Difficulty wise, I THINK that it was Hyrule Castle that was most difficult. More points towards PoT because it was amazing and well crafted. HC was a great endgame castle IMO.
I love the Arbiter Grounds in Twilight Princess. I feel like the boss was the coolest one in the series. Stallord rules!! It re-implemented the 4 poes thing, which was really cool. the dungeon navigation was so awesome, and I loved how the Sand Goddess appears twice. It is one of the biggest places for plot in the game, and I can't believe how detailed it is. I actually would scream like a little girl whenever the ReDeads would scream, because I would have little health left, and I just hoped that they wouldn't hit me (I know I'm pathetic). It is just the right length and it is very inovative. Cudos to you Nintendo; keep up the great Zelda games.
9. Palace of Twilight: Too short and very easy
8. Lakebed Temple: It's ginormous (did I spell that right?) and it was confusing following the water flow
7. City in the Sky: This wasn't a bad dungeon, but it didn't feel like it fitted into the game. At least the boss was awesome.
6. Forest Temple: This was a good dungeon, but the problem with this particular dungeon is the fact that it's a bit too hard for a first dungeon (that's my thought)
5. Arbiter's Grounds: This was a good dungeon with good puzzles. The only thing holding this dungeon back are the stalfos.
4. Goron Mines: It seems like you are just abruptly thrown into this dungeon, but I really liked this one. And whenever you meet up with one of the older Goron's, the Goron City theme would be remixed sort of like what Crash Bandicoot 2 did
3. Snowpeak Ruins: It seemed pretty weird having a mansion as a dungeon... oh well, it works. It may be a bit confusing getting around this dungeon, but like all dungeons, you get the hang of it. Also, I put this dungeon high on my list because of the boss (and for those who don't know, I won't spoil it)
2. Hyrule Castle: This one was great! The music was perfect, the puzzles were fun, and the final boss is very good.
1. Temple of Time: In Ocarina of Time, I always thought of the Temple of Time as a holding place for the Master Sword. Apparently, this game proves that this dungeon is more than that. The music is a generic tune and I like it for that (if that makes any sense). Also the puzzles in this dungeon are a perfect mix of fun and challenging.
I'm going to come back to this post as I refresh my memory but my favourite dungeon was the Snowpeak Ruins. I liked using the ball and chain, the way getting their through the snow was enjoyable and the use of unexpectedly friendly dungeon characters was a refreshing change (as opposed to monkeys or none at all). While heading into the boss room it was fairly predictable that the yeti would become the boss it was still one of the more enjoyable boss fights in the game.
While I didn't love the Palace of Twilight Sol's Hands take the top spot of most scary monster of the series for me (above Dead Hand then Re-Dead). They caused me a lot of trouble, mostly due to my own fear and partially due to their own difficulty.