The negadungeon is a dungeon where nothing good can come out of raiding the place. How can players tell a dungeon might be a negadungeon? It's been put behind sigils by ancient wizards or gods, it's full of traps to keep you out and the locals in, there's an army of guardians outside the place doing their best to keep you out, the king is going to have your head cut off if you go there, it hasn't been looted yet (really what is the place doing there just waiting for you?).
I'll admit it a fraction of my dungeons over the years have been negadungeons, it's in the source fiction. Plenty of places men were not meant to go and horrors man can not face out there. Just because it's on a grid and mapped out in 10' squares it doesn't mean it's a good idea to go there.
I've had players unleash a host of demons,eldritch horrors, and demigods over the years, recover treasure for a patron they probably shouldn't have, and set the stage for a faction to take over a dungeon that didn't have the resources to do it without the initial muscle the PCs provided.The negadungeoness of a negadungeon need not be exposed right away, or even this year it can come back to bite the PCs in their mail covered asses years later; horror works well when the familiar is turned upside down or put at risk.
The whole dungeon doesn't even have to be a negadungeon, do the orcs avoid "the black door" well maybe the PCs should also. Sometimes curiosity kills the cat. If everything in a dungeon is level appropriate, exploitable, or eventually vulnerable to the PCs it's a bit boring the campaign is doing away with all but casual caution and removing any hint of fear.
The negadungeon is a dungeon where the net result is "oh crap" there is no one way to get there but what a DM should avoid is the bad play experience while the players are dealing with the negadungeon. Everyone likes to think they would be the survivor in a slasher film, they'll be the ones who outrun the zombie horde, they will outwit the computer taking over the military industrial complex and that's what you want the players to think and feel as they are playing through a negadungeon. It's not a deathtrap for everyone, but its should at some point feel like is just might be.
So what sets a negadungeon apart from any dungeon, let's face it they are all horrible places to vacation ? Attitude and delivery, the typical dungeon has a clear hope of victory or profit eventually the PCs in a negadungeon are going to be looking for survival or a means to avoid the consequences of their actions. The notion that, this is dumb idea should be clear to some players and some point the creeping build up to this revelation is similar to horror and could likely unfold like a slow build horror tale. Temptation with little immediate reward may be a clue. PCs will be interfering not catalysts for positive change. NPCs will likely be seriously annoyed when they discover what the PCs were up to in a negadungeon. No one should be bragging about the negadungeon they romped through, it's best not to poke the memories with a stick. Many dungeons are oddly enough presented in an optimistic fashion, the reward for challenges overcome is the temptation. A negadungeon survived should leave the players waiting for the other boot to drop.