I can't really think of any right off the top of my head, but something I played recently was Thief 2. I know it's not an RPG, but the combination of puzzle-solving and reflexes in the game is just what I like in a dungeon. I don't actually own it, so I haven't played many of the levels, but the second one where you frame the sherrif is the best example of this

Also, an RPG Maker 2000 game called Dragon Destiny has awesome dungeon design, but that little maker is so rediculously small-time casual-developer low-tech as well as illegal that I doubt anyone actually cares about games made of it.

I think the forest temple in Zelda : Ocarina of Time is my favorite.
It's creepy, looks ancient, and could actually be an actual temple.


I think the key ideas to making a good dungeon or level is to make it seem like it has a purpose other than containing monsters.

Example 1:
Take a castle for example. The dark castle of the big boss. If it's a castle then it's built to act as a throne and defence to the boss running it. If you enter through the main entrance and walk straight ahead you get to the throne room. You do NOT end up navigating a labyrinth, forcing you to walk through the entire castle to get to the throne room. It got rooms with purposes, like a cantina and sleeping hall. It does NOT have a room there because there needs to be monsters there. Oh, and since it's a defence station of the boss - what odds are there that you'd enter through the main entrance? And what are the odds that you'd encounter a constant stream of enemies all the way to the last room?

Example 2:
Another example is a forest. The forest might have been there for millennia, in which case there is MOSS AND FALLEN OVER TREES all over the place. It does NOT look like it's been tended by a gardener this whole time. What if the forest hasn't been there this whole time? Well then there's other things lying around in it. Like the forest in the end of LotR : The Fellowship of the Ring. There's ruins and toppled over statues all over the place.

Key to design 1:
Building the dungeon after what monsters it's going to contain is something which equals bad level design. Why? Isn't this just my opinion? No, since it makes most players bored. It also reminds the player that somebody sat down and constructed this dungeon. "The reason those stairs have fallen down over there is to force me to take the long way". Either leave the stairs intact, or make it "The reason those stairs have fallen down is because of the huge hole in the wall here and the catapult-stone lying on the ground over there". Remember, the evil wizard wouldn't defend himself by collapsing a set of stairs would he? Your opposition would concist of whatever defence the evil wizard have set up - not some stairs!

Key to design 2:
Integration with the rest of the world. The said hole the the wall cannot just be there. Either there's a siege going on outside and they're flinging rocks at the castle as we speak, or the siege took place a long time ago. In which case there's evidence of the war elsewhere as well. Like broken catapults on the field out front, or lots more holes and rocks in the castle elsewhere.
When looking at the area of the dungeon from outside you can clearly see it's 100 square feet, but when you enter the dungeon it's suddenly 900 square feet. This makes everything seem artificial and made-up. This have been used so much that when a player encounters a place where it's actually as big inside as outside he/she's amazed.
If birds fly around on the field next to the castle, then birds fly around over the castle as well don't they? Aren't there normal creatures in the forest, instead of JUST monsters? If the monsters ate them, where's the carcasses?
And last, the player isn't the first person to ever walk here, right? If the traps are designed to protect something forever then they aren't likely to be one-timers, are they? In any case, you should be able to see some poor adventurers who have gotten stuck in them already. There's footprints around. The big monster of the castle who just happen to be in his lair today aren't always in there is he? There's evidence of his presence in the rest of the dungeon as well. Perhaps he goes out sometimes to eat some goblins, perhaps he leaves a slime-trail wherever he have walked. The monsters have probably left the dungeon before, leaving evidence of this around the entrance. It wouldn't be all sunshine until the very moment you enter, would it?

Summary 1:
Think "How did this place come into being?" instead of building the dungeon around the monsters.
Summary 2:
Compare the place to every other place in the world and check if it fits. Check if the details fit.

Alright, I've written enough now. Hope what I said made sense.
Laters!

Oh, and I would also recommend reading adventures for paper-and-pen roleplaying games. The place descriptions of Dungeons & Dragons and Eon are magnificent. They come in book form by the company, or webpage form by the fans. Search on Google. Just reading them gives you alot of insight in how to create a place. What you use them for doesn't even have to be fantasy even. You don't copy any features, you just learn what to think about when creating a place, be it a WW2 location or whatever.
You'd probably learn faster that way than by running around in dungeons in existing games. I highly recommend it.

[suggested adventure source by Google]