Technology is also my favorite general theme to use in dungeons. Whether it be the Great bay Temple in MM, the Tower of the Gods in WW, the Goron Mines, Temple of Time and Floating City in TP, the Mining Facility and Sandship in SS, etc., I find this to be a very intriguing idea in an otherwise medieval setting. I also like the fact that it can be combined with other themes to create a new dynamic on both.
Other than technology, I like dungeons that revolve around the undead, or of the more spiritual aspects. OoT and MM were amazing in this regard, while most of the latter games haven't quite got the same feeling to them. I think it's because they either rely too much on the disgust factor while leaving out the tension and dread beforehand, making the threat itself just ugly-looking, or they put all their effort into the presentation beforehand making you think this thing is gonna be seriously messes-up, but then when it arrives you sorta deflate and think "Wait, that's it? This isn't so bad."
The Dead Hand is my favorite example of it done right (the first time as a kid, anyway). You explore the entire house beneath the well before you face him (which is incredibly creepy, I might add), so your nerves are already shot. You go in, see the hands waving in the air, so you're dreading the fight that's about to happen. The only way to fight him is to let yourself become vulnerable by being trapped by the hands. And when he does show up, he's so horrifyingly... wrong, that you scream everytime you see him. (At least I do anyway, that freaking thing still gives me nightmares!)
So yeah, I'd like for them to do a dungeon revolving around the themes of the spirit and the undead. My idea for a dungeon would be one that actually kills Link from the very beginning. He becomes a ghost and must travel throughout the dungeon to get back to his body. Reuse that element from the Silent Realms, where you can't attack the enemies because they can kill you outright in one hit. But make it an entire dungeon that's focused on stealth and invisibility rather than action. You'll still have to solve puzzles like what we're used to in dungeons, but you can't kill anybody (at least, at first). Then the item you get much later on allows you to finally confront the enemies and keep them at bay, and it'll have much use outside of the dungeon as well, no TP crap. Only at the very end of the dungeon are you reunited with your body (I can't decide before or after the boss fight, a stealth-based boss fight would be very interesting to see happen, but the pure catharsis of beating the heck out of bid bosses like with Koloktos is also really fun).
It hasn't been explored a ton, but I enjoy dungeons that change shape or state as you move through. I've always thought it would be cool to have a grandfather clock-type level where nearly everything is moving around you.
This is also a really cool idea.