On Saturday, I posted about the deep weird—that dungeons should get progressively weirder and more unique the deeper the characters delve. I've been thinking about how I can implement that as a practical matter, especially in so far as giving the whole dungeon a unique flavor while giving each level a distinct but related flavor.
Leitmotifs seem like a natural device to accomplish that. In terms of dungeon design, the use of a recurring image, sound, smell, event, or map element would serve to immediately characterize the level and orient the player.
For example, if the big bad at the bottom of a dungeon was a group of mind flayers, all levels might have elements suggestive of tentacles. On this first level, there might be widespread tentacle-like vines, and kobolds who wield wavy-bladed kris. That level is ruled by an ogre who plays the bagpipes (which look a bit like an octopus). Throughout the level, the characters hear the playing of the bagpipes, long before they find the ogre. Bagpipes suggest a music motif, so the kobolds also sing rude songs. Stick a musical puzzle in there somewhere, and drop in a musical instrument as a minor magic item. As a bit of weirdness, the bagpipes can sometimes still be heard even after the PC's kill the ogre, and upon close examination the vines can be seen to twitch in rhythm to the music; the party may only notice this after they return from a deeper level. By dungeon level three or four, the carvings framing most of the doors (which were too worn-away to be recognized on higher levels) are a pair of tentacles that intertwine above the top of the door. If the players smell the stone tentacles, the stone smells faintly but distinctly fishy. Level five or six could have a sea theme (with the sound of water audible in certain places on the level above). The entire level smells of salt and seaweed. Most of the passages are natural twisty caves that lead to an underground sea overgrown with brain coral. A giant octopus lives there. Perhaps a room on this level is only accessible if the party approaches it using a peculiarly circuitous route they found mapped on a wall two levels above.
So, the overall motif of the dungeon is twists and tentacles. The motif of the first level is music. Both motifs should trigger associations that orient the players in your dungeon. These are off-the-cuff examples, but hopefully you get the idea.