Darkness is associated with evil, ugliness, scary monsters, and super creeps. This is the reason for the naming of The Dark Side and why Evil Counterpart characters and certain Underground Monkeys often have 'dark' in front of their names. Like all Colour Coded For Your Convenience/Good Colors, Evil Colors examples, this is common, but not universal, and will vary from culture to culture.
The logic behind the trope is as follows: most humans fear the dark, at least to some degree; our sight is the sense we depend on the most, and we cannot see well in darkness, therefore a lack of light makes us feel very vulnerable to danger.note Leopards, one kind of predator our ancestors had to deal with on the African plains, prefer to hunt on moonless nights so that they can sneak up on their prey. Humans that weren't afraid of the dark probably became leopard chow. Furthermore, the fact that it's so hard to see in darkness (well, for humans, anyways) has caused some of us to associate darkness with deception. Evil is associated with deception as well, so, from Star Wars to cowboy movies, a lot of bad guys wear black hats. If you want to be even more obvious about it, give the bad guy a name that has something to do with darkness.
If a character has darkness-based powers, see Casting a Shadow.
Stories where Dark Is Evil and Light Is Not Good are commonplace to show that the light can be just as foul as darkness.
Why Evil Is Not Well Lit, and why having the sun vanish is a bad sign. See also Light is Good, Bad Powers, Bad People, and Obviously Evil.
Dark Is Not Evil is the inversion and the good counterpart of this trope. Another one is The Sacred Darkness, where Dark may or may not be evil, but is just as important as Light.
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Ditto with the Ruler of Darkness, Hayate's completely Evil Twin that was formed from the remnants of the Darkness of the Book of Darkness during the climax of the Battle of Aces video game.
Mai Otome: the main antagonists use dark-themed GEMs. Nina Wang has an Ultimate Black Diamond, which is said to be representative of her "extreme and mostly selfish" bonds with Sergay and Arika, which is the opposite of the selfless bond between Master and Otome exemplified by the original Pure White Diamond. Tomoe and the rest of the Valkyries use Cursed Obsidians of the Darkness, and Schwartz, named after the German word for black, is evil.
Yu-Gi-Oh! GX: Darkness/Nightshroud twists thesetropes for all they're worth. Since dark in the Yu-Gi-Oh universe is stated to be a form of raw potential that is moulded by human hearts, Darkness/Nightshroud is implied to be created from The Sacred Darkness specifically because humanity thinks that Dark Is Evil.
Magic: The Gathering: Black follows traditional "evil" aspects, like death, necromancy, demons, poison, plague, etc. However, the staff puts a lot of effort stating that Black itself isn't evil. It's just that 90% of the things associated with it are.
Marvel has Dormammu and Umar, rulers of the Dark Dimension. It's been implied that the Dark Dimension is something of a Fisher Kingdom, however, and millennia of Dormammu's rule has made it into the nasty place it is today.
Also from Star Wars, Darth Vader wears a dark costume in the original trilogy and Darth Sideous wears a cloak so his face is in shadow. Word Of God is that Luke wears a light costume and it gets progressively darker as he goes from innocence to accepting the dark side as something that exists and overcoming it as opposed to avoiding or destroying it.
In the prequels, Anakin favors darker clothing than the rest of the Jedi Order, even before his turn to the Dark Side.
Nosferatu has a pale villain, but he wears a dark coat and needs darkness to survive. It's from this film that all modern legends of vampires and daylight not going together stem. In the original novel, Dracula was able to walk around in human form in the daylight.
Deconstructed sharply in Spike Lee's biopic of Malcolm X. In the prison library scene, Charles Dutton's character gives a monologue about the implicit association of darkness with evil and lightness with good in the English language, which has a profound effect on the man who would later name himself X.
In "How to Murder your Wife", Jack Lemmon's Italian bride stays up late watching American movies on TV and keeps asking "Which are the good guys, the white hats or the black hats?" I think that whatever she knows or doesn't know about America, that's one concept she would certainly have learned in Italy.
In Rise Of The Guardians, Pitch Black is the main villain (he's also known as the Boogeyman and the Nightmare King. He is basically the living essence of fear, and has dark grey skin, black hair, and black nightmare sand.
Dark Creatures or "Demons" (as explained in Fantastic Beasts and Where to Find Them) consists of any creature that can use magic and mainly uses said magic for malicious intent. Dementors are the most promenent members in the books.
And before him was his own master, Morgoth (which means "The Dark Enemy of the World"). Some of Tolkien's unpublished writings imply that dark is associated with evil because Morgoth's ultimate goal is to tear down the world until it is reduced to the original primordial void.
Notably averted with Tolkien's Dark Elves, the Moriquendi. While "Dark Elf" has come to mean evil in nearly every subsequent High Fantasy, the Moriquendi are simply Elves that never went to Aman and never saw the light of the Two Trees of Valinor. They're just as good, if not better, than any other group of Elves and are even represented by one of the most popular Elves ever, Legolas.
In The Wheel of Time, the Big Bad is called the Dark One (there are also other names, but Dark One is the most common one) and the evil side, i.e. everyone and everything associated with the Dark One is referred to as Shadow. Human servants of the Shadow are called Darkfriends, one name for the creatures that command the universe's Orc-equivalents is Shadowmen, and...yeah, maybe you get the point by now.
According to the movie adaptations of Chronicles of Narnia, the Pevensie children are divided in two categories: Peter and Lucy, who are fair haired, are the good kids compared to Edmund and Susan, who are dark-haired and fall to the dark side at least once (Edmund betrays his siblings to the Big Bad and Susan falls into disgrace later, when she refuses to believe in Narnia anymore and is left outside Heaven - aka Narnia).
The Dark Faery court from Melissa Marr's Wicked Lovely series. Although, this is possibly a subversion - they are more cruel than evil and need to be to survive. They are essencially emotional parasites, but Irial truly loved Niall and Leslie (although he was very cruel to them, using Leslie as an emotional conduit and stripping her of emotion and free wiil and allowing his servants and guards to both phsically and sexually abuse Niall), and although Gabriel comes into the 'abusing Niall' category, although only physical, he was NOT one of the fey who raped Niall - this is a common misunderstanding - and can be incredibly kind to his halfling children. Niall himself comes more under Dark Is Not Evil, although the injustices of the past push him more and more towards the moral grey area Iri and Gabe occupy.
Prevalent in Madeleine L'Engle books, starting with A Wrinkle in Time, where the Black Thing covers the world of Camazotz and threatens the planet Earth. In later books, the Echthroi (repeatedly refered to as "the powers of darkness") also gain an association with a horrible sound and a disgusting smell.
In Warrior Cats, when villains die, they go to a forest of pure darkness.
Also, most of the main villains have been dark brown tabby toms, for some reason. Even Thistleclaw, a gray and white cat, accidetally got described as dark brown a couple times. Once fans pointed this out, villains began to have different pelt colors: Sol and Mapleshade are torties and Dark Forest cat Snowtuft is white.
Averted in Diana Henstell's NEW MORNING DRAGON, where the Devil insists on wearing white suits at all times.
On Buffy the Vampire Slayer, the outfits of many vamps take on this trope. Also, The Bringers, servants of the First Evil, all wear black robes.
On Lexx, His Divine Shadow might as well wear a placard around his (black-clad) neck announcing that he is an Evil Overlord. Between the title, the black robe, and the decor of his planet-sized Evil Tower of Ominousness, it's pretty obvious.
Lost: an extremely blatant example—Jacob wears white and the Man in Black/smoke monsterwears black.
In a TV movie on the making of the Vietnam Memorial in DC, people kept objecting to it because it's black and therefore bad and makes their sacrifice seem bad. A black army officer stands up and reminds him of his years of service and that if anyone makes another comment on how "black is bad" they are going to take it outside.
In Babylon 5, the Psi Cops wear all-black uniforms, the Nightwatch wear black armbands, and the Shadows' ships are blacker than the darkest night. Londo's costume also subtly darkens as he becomes more involved with the forces of chaos.
Morgana Pendragon in Merlin started dressing like Bellatrix Lestrange in season four. In season five she strays from the Bellatrix look, but continues to wear black from head to toe.
Agravaine wears black.
Uther Pendragon is usually dressed in dark clothing as well.
BIONICLE plays this straight, but also subverts it: every character in the Matoran Universe has an inner balance of light and shadow. Those characters that tap into their dark side or are drained of their inner light turn evil as a result, gaining shadow-based powers and becoming darker in their coloration. At the same time, thanks to Color-Coded Elements, some element-based good guys also sport dark colors and a handful are almost completely black.
Darkrai. Freaking Darkrai. Did I mention he tells you to go kill yourself?
Also, "Dark", the English name of one of the 17 elements common to all Pokémon, was localized directly from "Evil", as the type is known in Japanese. This explains why many moves of the Dark-type involve doing immoral things like stealing or lying or having "bad thoughts". Though the type had relation to darkness even in the original games, such as Eevee evolving into Umbreon at night.
Subverted in that not all of them are evil. Mightyena (a hyena/wolf mix) is very loyal to a skilled trainer and Absol is just plain misunderstood.
The Dark Elves are the evil guys in ZanZarah: The Hidden Portal, though there is an additional distinction between Darkness and Chaos and The Man Behind The Man is of the Light Is Not Good variety.
Opoona follows this quite heavily, to the point that most people can't even enter true darkness without serious damage to their mind and body. Justified in that it's actually The Corruption, created by the ultimate Big Bad of the setting, though not the game itself.
All of the Prime Evils and Lesser Evils of Diablo are this. They are all full of evil and that is just a topping.
The The Heartless are the manifestations of the darkness in capured hearts.
Even after Riku reverses his Face Heel Turn and uses darkness in heroics, he prefers to think of himself as 'darkness that leads to light' and that's why he calls his keyblade 'Path to Dawn' instead of 'Path to Twilight' like DIZ guessed.
In the sequel, it is revealed that Hazama / Terumi Yuuki is this as well by virtue of his nice, black suit. Mu-12, who calls people by expository titles, refer to Hazama as "The True Evil", indicating that he is even worse than the Black Beast itself. (Those who have played the story up until that point probably gloss over this as a Late Arrival Spoiler, though, because they've already seen what Hazama is capable offirst hand.)
In Minecraft, enemies spawn in any dark areas (whereas non-enemy animals spawn on grass in the light).
In Warriors Of Might And Magic, you can't learn Dark spells, and the few swords imbued with the dark element aren't really strong. Furthermore, Skeletons, Ghouls, Undeads, Wraiths, and Demons have the Dark Element with them.
The RPG series notes that Dark magic isn't evil as such - it is how you use it that is important - but it includes spells whose casting can be called evil no matter the circumstances (sacrificing a hireling for a temporary advantage!) and is associated with the Path of Dark, a religion/philosophy that nigh-universally seems to attract cruel people that want to do bad deeds.
The Half-Life 2 mod Black Snow takes things to extremes: light, warm areas keep out the thing that's chasing you around the research center. It turns out that the thing is a predatory strain of fungus that can thrive in any environment but well-lit ones.
The Darkspawn of Dragon Age. The Taint that created them originated from the corrupted Golden City in the Fade, now known as the Black City. Subverted slightly in Awakening with the appearance of intelligent Darkspawn, but even then, the more antagonistic faction of the awakened Darkspawn wear black armor.
This deserves further clarification—the original IV equates dark-elemental abilities with The Dark Side, even having the dark-elemental protagonist's "Spirit" score drop as he levels up and becomes more hardened. As part of the plotline, he's eventually required to give up his powers and Level Drain with light-elemental abilities. Final Fantasy IV: The After Years goes a more balanced route—having been unable to completely purge his dark side, the hero is ultimately forced to accept and control it. Dissidia: Final Fantasy takes this all the way to Dark Is Not Evil.
It's still up in the air where Sinfest falls in regards to this—devils aren't always evil, but the capital-D devil definitely is, and his influence is highly corruptive. (Then again, Light Is Not Good is in effect as well—the most moral characters are the ones who seek some form of balance.)
The main villain from Samurai Jack, Aku, is essentially a giant shadow demon, and things under his control are often artistically depicted as being wrangled by black veins. There's another element to his darkness as well, with robot enemies having black thick oil instead of blood, and his effect on the corrupting effect on the world is a pollution of it in some cases.
Both subverted and played straight with Raven from Teen Titans. She's not evil, but she is part demon, and that's the side of the family her powers come from. This means she has to maintain incredibly strict self-control, especially while using said powers, lest she lose control of them or, worse, unleash her Superpowered Evil Side.
In Allegro Non Troppo 1, all the animals are brightly colored and cartoony, except for those jerk-face apes with red eyes and black sclera who wreck the planet as they become human but remain vicious animals on the inside. Averted in the beginning with the black proto-blob, unless evolving out of human trash counts as evil.
Nightmare Moon from My Little Pony: Friendship Is Magic played this very straight, being a jet black Mad God who usurped Princess Celestia and plunged the world into eternal night. While her true self, Princess Luna, isn't evil, Word Of God confirms that the rest of Equestria is still afraid of her partly because of her actions as Nightmare Moon and partly because they still believe in this trope. King Sombra takes this trope even further. He is described as having a "heart as black as night" and was able to subjugate an entire empire on his own with dark magic.
In The Super Hero Squad Show episode featuring Chthon (a grey, wrinkled, vaguely demonic man with claws, pointy teeth, and glowing eyes)...
Iron Man: So, what's your prognosis, Doctor?
[Doctor Strange sizes up Chthon, who is cackling and rubbing his hands]