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So - you want to make a dungeon. You've got some cool ideas, an awesome map, even found something horrible from the Monster Manual for a great boss-fight for the end.
But what is your dungeon?
The theme of your dungeon helps to figure out why it's there, what's in it, and what the players will do once they get there.
Location-based dungeons can be easy to theme. Say it's a Wizard's Tower - you need some weird magic-based monsters (Living Spells, unusual Undead, Owlbears, Animated Objects), unusual traps (either traps explicitly made using magic, or "natural" hazards like pools of pure elemental matter, doorknobs that have been supercharged with electricity, etc), and some cool set-pieces (like a battle that occurs in a room with no gravity, or an area that continually shifts between the different Elemental Planes, or a series of rooms hooked up via teleportation gates).
Another easy way to work out your dungeon's theme is to think what type of creatures might inhabit it. For a classic example, The Crypt Full of Undead. You've seen it so many times, the ideas practically roll onto the page unbidden (creepy surroundings, no light sources, a few cursed items, skeletons, zombies, a couple of souped-up versions like Ogre Zombies or something such, weird encounters, spirits, bugs, ancient yet still functional traps, etc). While it might seem cliche, you can mix it up a little with underused monster types - an all Aberration dungeon (maybe a cave system with a link to the Underdark or Far Realms) could be really interesting, as could the legendary Ooze-based dungeon (you don't want to know where they all came from...).
Picking a theme, however, should mean more than picking monsters out of the books. If you do take Aberrations as your theme - did you pick them because they're weird? If so, make sure the dungeon reflects that. Non-Euclidean geography, maps that lie (or areas that constantly change shape), the chance of madness for PCs, a few mind-screw elements here and there... really amp up the theme of weird. If it's a tomb full of Undead, is your theme Horror? If so, make sure the descriptions of the Undead are terrible to behold, that there are hints of their past lives (or perhaps the suffering they are/were going through before becoming shambling horrors).
Even try and add a little fright into the metagame, by using Undead the players are not familiar with - whether from more obscure books, or made up yourself (and because I love to plug his awesome work, Dyson Logos has a great table for Unusual Undead Abilities) - when your players face off against a horde of zombies, only to find out each of them can teleport, or throw lightening bolts into the group.
Similarly, if you want to take things down a Cliche route for laughs, then ensure that everything's been done before - there's snakes (why did it have to be snakes?), mummies, trapped sarcophagi, legions of skeletal warriors, and dark wizard at the end... you know the drill. Try and add some light-hearted elements, like an Obviously Evil Bystander who turns out to be the villain, some comical mid-dungeon NPCs, whatever you want to reinforce the idea of humour.
My theme for this dungeon will be "Magic and Illusion" - as such, I'll be making a (not-so) Abandoned Wizard's Tower, which allows me quite a lot of leeway in how I go about it!