The artificiality of dungeons is important, I think, the hand- (or claw-, or tentacle-) made -ness of them. The idea is: you are alone--but someone was here before you.
A key thing in making dungeons feel dungeony is inspiring the idea that anything could be down there. The ship in Alien and the Borg cube in Star Trek--these are not quite dungeonish to me, because you already know what's down there--dangerwise anyway--more Borg, some Alien. They lack that intimation of unknown potential. The best story about dungeons is The Library of Babel by Jorge Luis Borges. It's about a library that...well I won't spoil it. But I'll quote it:
"Before, there was a man for every three hexagons. Suicide and pulmonary diseases have destroyed that proportion. A memory of unspeakable melancholy: at times I have traveled for many nights through corridors and along polished stairways without finding a single librarian."
Isn't that exactly what playing a dungeoncrawl videogame alone in front of your machine at 4 am is like?
Some other examples:
Bowser's castle in Super Mario feels even more dungeony than it should. Yes, Super Mario is a happy, friendly game with smiling clouds, but the first time you get to the Bowser level, the music changes and you realize, all of a sudden, that you kind of miss all the smiley mushroom men that were trying to kill you on all the other levels, and the music has changed, and now you are alone. (Which you were all along.) And it's creepy.
As many people have pointed out, Alice In Wonderland reads very dungeony--grow big so you can reach this keyhole, shrink down so you fit through that door--but it didn't look dungeony until American McGee put out that very gothy Alice video game and there was the chess level in there--it's all black and white with huge chess pieces that come at you bleeding red.
Caves--organic, natural caves, do nothing for me. I like a manufactured dungeon. On some level, the decayed geometry--right angles, perfect circles, pointed arches (all crumbling)--communicates to your DNA. It says: something has been here before--something intelligent. It was probably smarter than you or at least managed to move and shape more earth around than you could--and it died anyway. I tend to think of a dungeon as somehow metaphorically like the inside of your brain. Running a party through a dungeon is kind of like running them through the DM's head. If there's a shard of black glass in someone's pack is that automatically a clue or is it possibly just for atmosphere? Can the traps be turned against the monsters in the dungeon? Can the monsters be turned against each other? Is there a "right way" and a "wrong way" or are there many right ways? Depends on what's in the DM's head. "Crawling" is an important part of dungeons. If you can fly, or are so big you can knock down any wall, or you can turn into living liquid, then you might not notice one of the major features of dungeon aesthetics, which is the architecture itself is out to get you. I don't mind people playing monsters in a game--as long as they don't play a monster so enormous or versatile that the architecture ceases to scare them. A palace can feel dungeony, as long as you make it feel like it's so big that even whoever owns it doesn't know what's going on in there. And it's hard to get out. And you can't see anyone out the window.
I never liked the idea--strongly implied in the early rules--that the standard drill was to go into the dungeon, then leave whenever you needed to rest in order to heal or recharge spells. The idea that you could leave whenever you want seemed to domesticate the dungeon too much. Plus it meant you had to go to a town which...well towns are all well and good but they're not dungeons. At least not usually.
So, the way I set it up, the players generally end up sleeping in the dungeon. The downside is someone or something will probably try to kill them in their sleep, but the upside is, in order for them to have fun, I jiggered the rules a little:
_If a wizard sleeps a few hours, wakes up, kills something, then goes back to sleep, I say that still counts as full rest.
_In AD&D, once you're at 0 hp, you can recover but it takes at least a week. Leaving in the middle of the dungeon to go back to an inn for a week and re-tool kills the dungeon-as-mythic-underworld mood. So,if you survive the night, and get bandaged up, you get a hit point back.
(images, top to bottom & left to right: Ian Miller, Dave Trampier, 2 more Ian Millers, HR Giger, 60s edition of Borges, some temple in SE Asia, the city of Valetta--world's dungeonest city--on Malta, Giacometti, a bunker from Paul virilio's new book on bunkers, Marble Madness, 4 drawings by some guy,2 comic pgs by P. Craig Russel, painting by Bihzad)