Frequently, when a character enters an evil or cursed area, they'll find that it smells really, overpoweringly bad. It usually smells of rotten flesh (or just "death") and grows more powerful as the investigator gets closer to the threat. Another variant is an evil being carrying a bad stench with it when it appears. Frequently one of the Horror Tropes.
This trope stems from the fact that dead and unclean things smell bad, so if somewhere or something smells bad, it's probably dangerous. The belief that demons smell of sulfur is also a contributing factor.
In The Tough Guide to Fantasyland, Diana Wynne Jones refers to this as the "Reek of Wrongness," which can take many forms besides just smell.
Compare with Uncleanliness Is Next to Ungodliness, where the stench is just a character's poor hygiene.
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Anime & Manga
In Fruits Basket, Kyo's true form smells so bad that Tohru vomits the first time she encounters it. How evil it is depends on who you ask, but the consensus is that it is NOT friendly.
Watanuki from ◊◊◊HOLiC came across some situations like this, but he's the only one who can sense it. One example is at Himawari's friend's school where the game, Angel, is taking place. Domeki can't smell it. It's like some sort of spiritual stench that only Watanuki can smell, and it got worse as he got closer to the threat taking hold.
The very first chapter of Black Joke features two homosexual assassins that use disgusting amounts of perfume. In the climax its shown billowing inside a car in thick, choking fumes.
Michael: Mother, this cloth... it smells of death!
In Gary Jennings's Aztec, the Spanish conquistadors rarely bathed, according to the European customs of the time (mid-to-late 1400s). This in contrast to the frequent bathing and saunaing habits of the Mexica. In one scene, Mixtli has them hauled into the yard and washed by force, which terrifies the invaders.
In the short story "Jerusalem's Lot" (set presumably before 'Salem's Lot) by Stephen King, all the buildings in the eponymous village smell terrible inside. This is probably due to the giant worm living beneath the church.
Also shows up in another King work, The Dark Half. A policeman inspecting the car George Stark had used earlier notes that it smells hostile and animalistic. Stark also falls into this trope later in the book, being followed by the stench of his own decaying body.
In James Joyce's A Portrait of the Artist as a Young Man, Stephen, as a part of his education, goes to a mass where the priest gives a long, heated speech about the horrors of hell, including the eternal smell of decaying corpses.
Most of H.P. Lovecraft's eldrich horrors are described as smelling rather icky.
The Necronomicon: Iš Shub-Niggurath! As Foulness shall ye know them!
A Wind in the Door and other books featuring the Echthroi as villains always mention how bad they smell - "makes silage smell like roses," according to Calvin. Thing is, they can disguise this smell until they are found out.
In A Swiftly Tilting Planet, Chuck has a very sensitive sense of smell, and cruel, mean people smell distinctly bad to him.
In Dracula, the eponymous villain has foul breath, almost certainly due to his diet, and areas where he stays are, well, to quote the book:
"But as to the odour itself, how shall I describe it? It was not alone that it was composed of all the ills of mortality and with the pungent, acrid smell of blood, but it seemed as though corruption had become itself corrupt."
The regions of the world corrupted by Torak and Zandramas in The Belgariad and The Malloreon are reminiscent of Mordor: blighted wastelands overrun with fungus and other unwholesome things, and they absolutely reek.
While not technically truly evil at heart, Erik from Gaston Leroux's novel The Phantom of the Opera is described by Christine as having hands that smell of death.
Very frequent in The Lord of the Rings. To give a few examples, Shelob's lair was extremely odiferous, and the flowers growing near Minas Morgul were described as smelling like rotting flesh.
In L. Jagi Lamplighter's Prospero Lost, Mab reports an evil smell - like one of the lords of hell, whom he is familiar with.
Well, technically, it's more chaotic, but Free Magic in Garth Nix's Old Kingdom series is extremely dangerous and almost always wielded by nasty pieces of work, and it's described as producing an acrid, hot-metal smell.
"He imagined he could smell the decay in the Emperor's worn body. Likely that was just a trick of the recycled air, run through dozens of filters to ensure that there was no chance of any poison gas being introduced into it. Filtered the life out of it, perhaps, giving it that dead smell."
Break of Dark by Robert Westall has a short story about the ghosts of a trio of loathed relations. The first signs of their malign presence involve an otherwise squeaky-clean house become beset with the smell of old woman and breath mints.
In The Hunger Games, President Snow smells like roses...and blood. There is an actual reason for both, but still...
An evil reason.
In Philip K. Dick's The Divine Invasion, the protagonist finds a poor, lost, talking baby goat. He slowly becomes aware of a terrible stench surrounding it. It turns out the goat is actually Belial.
Infected in The Troop smell like rotting peaches, because their bodies' metabolisms are supercharged; and are breaking down their body tissues to sustain itself and the mutant tapeworms in their stomachs.
Live Action TV
In Supernatural, ghosts leave a smell of ozone and demons smell like sulfur.
Buffy the Vampire Slayer - In "The Zeppo", Giles is seeking supernatural aid in a graveyard; Xander spots him and tries to join in the apocalypse-fighting to get away from new 'friend' Jack and his dead pal Bob.
Giles: There's something different about this menace. In the air, I can feel it. The stench of death.
Xander: Yeah, I think that's Bob.
While Boogeyman was known for appearing unexpectedly, either as part of an ambush or because someone called his name, sometimes he felt the need to let everyone know of his arrival, which he usually did with a stick which overflowed with an orange smoke is said to have reeked.
In Werewolf: The Apocalypse, Gaia Garou Theurges can detect Wyrm presence through the gift Sense Wyrm. Many liken the Wyrm's presence to an odor. Mari Cabra complained that a bane-infested Umbral location stank of the Wyrm.
Diablo. Upon entering the catacombs, the main character comments, "The smell of death surrounds me."
The interior of the Giant Worm in Gears of War 2 is stated as smelling terrible. Since the worm is essentially a mobile disaster and a place where one member of the squad meets a gruesome death, this trope is in full force.
In the Resident Evil 5 DLC story "Lost in Nightmares", Jill and Chris enter an area where there is a really bad smell. Chris states that he hopes that they don't run into whatever's making it. They do. A monster with a bloated back, wielding an ax and a horrible stench.
Blizzard seems to love this trope in general. In Warcraft III, it is not uncommon to hear some characters say they "smell the stench of demons" somewhere or something else along those lines.
A few shorts of the Japanese horror anthology "Tales of Terror From Tokyo" dealt with this trope, including "The Smell", where a young girl comes upon a kneeling woman who always faces her back and stinks of rotting meat (for some reason, the smell prompts her to try to call the police right before the ghost woman does her wacky hijinks on her ), and "The Smell of Animal", where the visiting niece is the only character who finds her aunt's husband has a horribly repulsive smell. Through flashbacks, it's revealed that, in his youth, the husband enjoyed killing animals as a hobby and the smell latched onto him .
The Grim Adventures of Billy & Mandy: A sleepless Billy imagines his own bed time story where there was a town so happy that it Tastes Like Diabetes watched over by an evil wizard. A few changes to the story caused the wizard to become fat and smelly, much to his chagrin. The wizard makes a Heel-Face Turn in the end when he finds out how happy they are.
David Sedaris says that crickets don't just smell bad, they smell evil.
According to veteran stories, battlefields stink. Burnt wood, metal and rubber, rotting dead bodies, burning oil and fuel, decay and mud. Burying the dead and removing the debris from the fields is a foremost task in the aftermath of a battle, before diseases set in.
Pirates, like most sailors at the time, would sometimes go for days or weeks without bathing due to the lack of clean freshwater on board their ships.
Reportedly, you could always tell when a slave ship came to port; they stunk to high heaven with the combination of human waste, blood and other substances resulting from their chained cargo and their crews were often the worst paid and behaved of any kind on the sea.