Okay, so you have a villain who is legitimately intimidating and frightening. Maybe they try to destroy all positive emotions, or maybe they turn people into twisted shambling abominations, or maybe they're plotting genocide. Point is, they're actually a fairly creepy villain. The irony is that they're stuck in a Sugar Bowl.
As one could probably tell, this trope is about villains in normally lighthearted fiction that are so disturbing, or even terrifying, on some level that they kind of clash with the tone of the show/game/whatever. Because of this type of villain's ability to ruin the mood of the story they're in, this trope can overlap with Knight of Cerebus or Complete Monster. If a series has a lot of villains like this, then it's taking a ride on the Cerebus Rollercoaster.
A violation of Genre Consistency. Compare and contrast the Crapsaccharine World, where it's not just the villain, but the entire world that is rotten to the core. A major cause of Sugar Apocalypse and Surprise Creepy.
In the first ten or so volumes of Pokémon Special, the adorable art style makes everything like childish and cutesy. This doesn't stop the Yellow arc from involving a villain bent on genocide of all humans.
The Big Bads of the Pretty Cure franchise are usually like this. One of them is an entity that existed before everything and wants to plunge everything into nothingness, another is a life-hating Eldritch Abomination that turns every planet he visits into sand dunes, yet another is a monster born out of humanity's collective negative emotions, etc etc... This is a series that is (supposedly) for little girls in elementary schoolyears.
Fruits Basket is an adorable series about a cute high school girl who befriends a lot of pretty boys and the hijinks that ensue. Then we are introduced to Akito, who we learn has been committing various forms of physical and psychological abuse on various family members, and has no problem with doing the same to any "outsiders" who look like they're butting in. Later, Akito actually becomes sympathetic when her mother, Ren, is revealed to be even worse.
Although it's about World War II, Axis Powers Hetalia manages to be pretty goofy while focusing on the general incompetence of the nations. While there is fighting, it's portrayed as comical punches and cartoonish damage. In the movie Paint it, White!, we are introduced to invading aliens called the Pictonians. The Pictonians quickly conquer nearly all of Earth, transform most of humanity into their species, and abduct them as slaves. Everything the nations do to fight them fails, and they very nearly lose at the end, when all of them but Italy are turned into Pictonians. While screaming.
Kagato from the original OVA and Tenchi Universe was no slouch himself.
The original Dragon Ball was considerably more lighthearted than the much more well-known Dragon Ball Z. Most of the villains were dealt with comically, and only a few were shown to pose a serious threat to Goku and his friends. Then came Tao Pai Pai. Tao Pai Pai is a Psycho for Hire who cares only about profit and ruthlessly and remorselessly wipes out anyone who gets in his way with his bare hands. After he murders Upa's father and defeats Goku in battle, he laughs at Upa and tells him that he's lucky that he's still alive, meaning that he has absolutely no problem killing children. One of his worst offenses has got to be when he forced a tailor to overwork on making an outfit for him in about three days...which he rewarded by killing him. When he returns to Karin's Tower to look for the one Dragon Ball he neglected to find, he grabs Upa and throws him against the tower (fortunately, he was saved by Goku). After his defeat, he was rebuilt into an Ax-Crazy cyborg who wanted nothing more than the deaths of both Goku and Tenshinhan. He's arguably the Knight of Cerebus for the entire series. While the Z Fighters heavily outmatch him in Dragon Ball Z, he still has no redeeming qualities.
Les Légendaires is a seemingly kid-friendly comic book, involving a world where everyone has been turned into children following a magical accident. The characters are typically comical (though they do have moments of Bad Ass), and the universe even more. But let's have a look at the main villains:
Skroa is a bird-like demonical sorcerer that used to be Darkhell's rival and frequently uses the protagonists as pawn for his plans. Is shown slaughtering a group of armed human beings of his own. He once cut his own arm off as a part of his plan;
Transformers: More than Meets the Eye is a fun and adventurous series with a cast of funny and lovable characters. The main villains are the Decepticon Justice Division, a group of homicidal and sadistic extremists who torture and murder anyone who so much as questions Megatron's ideology. Their leader Tarn is the most vile of all, manipulating and using others to feed his addiction to transforming at the same time he's torturing people. They're the only villains who are played straight, and don't have any Freudian Excuse or heroic endgoals to justify or explain their horrific actions.
Then there's Overlord who's motivation doesn't even have the perceived nobility. His goals and reasons boil down to "Killing is fun". He goes about murdering and maiming in one issue after we find out his backstory.
Ironically, this same arc also sees Chrysalis used for comedy pretty often (due to her interactions with the aforementioned CMC), while in the show she was played completely straight at all times.
Another arc presents a Mirror Universe, now presenting the heroes and the normally kind princesses as taunting and vengeful antagonists.
Loki: Agent of Asgard is, so far, light-hearted series for Marvel standards, yet, the Big Bad is Old Loki, in his clasic incarnation, sinister and vile as usual.
In Marvel and DC superhero comics this can happen by Rogues-Gallery Transplant. Characters like Mephisto, Nightmare and Shuma-Gorath in Marvel are all really dark villains, but they also moved from antagonizing characters like Ghost Rider and Doctor Strange, where they aren't out of place, and are now general threats to entire Marvel Universe. Which means sometimes they can show up in much lighter series, while retaining all their usual qualities (through Mephisto and Nightmare can ram up Black Comedy a bit to fit better). Case in point, Mephisto showed in abovementioned Loki: Agent of Asgard, Nightmare was an antagonist in pretty comedic Fantastic Four story and Shuma-Gorath fought Mighty Avengers in straight superhero adventure.
Were Back A Dinosaurs Story is a cutesy film about dinosaurs being sent to our time to make children happy. Nothing scary about that at all. Well, except for the creepy old scientist Professor Screweyes, who runs a Circus of Fear, has children sign a contract in their own blood, and is eaten by birds at the end of the film.
The Evil Queen (Grimhilde) from Snow White and the Seven Dwarfs, while most of the film is very cutesy and whimsical, she takes her pursuit to preserve her narcissistic self image to dark extremes. She ordered her Huntsman to assassinate Snow White and bring her heart as proof of the deed. When he failed, she took matters into her own hands, becoming a frightening looking hag who conducted a poisonous apple that would've put her into a deep sleep. Her response was that her caretakers, the dwarfs would've buried her alive, not knowing the truth.
Maleficent from Sleeping Beauty. The story was very lighthearted till she showed up and sentenced baby Aurora to death for a petty reason, though it is more likely it for the hell of it. All the heroes could do was stall for time, which only worked because her minions thought babies stayed the same age, but once she sends her raven, Aurora is soon ensnared by her powers and is put into a deep sleep by a spindle created by Maleficent. She captures the one prince that could undo the spell and have him wait for a hundred years so Aurora would go mad from the sight of an aged and broken man, implying that even with the counter-curse to her death sentence, she could twist it to something worse. And since she is so high in the Sorting Algorithm of Evil, and by high, she is easily a Reality Warper who was so beyond the heroes in power, that the fairies had to cheat along the way in order to even do her in. She also turns into a scary dragon with power to match that almost manages to defeat the prince, "almost" meaning the fairies had to intervene in order to even land a deathblow.
The Disney version of Claude Frollo from The Hunchback of Notre Dame is, for all intents and purposes, a medieval stand-in for Hitler. The movie was already more adult than is normally thought of for Disney, but it was still shocking. More disturbingly, Frollo is one of the most realistic Disney villains ever produced, and he doesn't have an iota of comedic qualities. There's a reason why many see him as the darkest villain the company has ever made.
The Princess and the Frog gives us Dr. Facilier, a voodoo witch doctor willing to sacrifice all of New Orleans to pay off his debts to dark voodoo entities. Although he gets in on the light, jazzy theme of the movie with a cool Villain Song, it's still clear that he's selfish, relentless and bad to the bone. That he murders the comic relief in cold blood on screen cements this. And then there's his Family-Unfriendly Death...
Though the Coachman is far worse, Stromboli is pretty bad too. Both his and the Coachman's actions can be Nightmare Fuel.
Oliver & Company is a very lighthearted movie, featuring talking cats and dogs. However, the storyline is a loose Setting Update of Oliver Twist, and its human villain Sykes — the counterpart of the novel's Bill Sykes — is a Loan Shark played utterly straight. There's nothing cool, funny, sympathetic, or even hammy about him. He's just a cold-blooded thug who wants his money now and doesn't care what he has to do to get it.
Jafar in Aladdin has shades of this. Because the movie was an action-packed zany comedy, animator Andreas Deja decided to keep Jafar very subtle in contrast. (This can be seen in the art style. Nearly everything else in Agrabah has soft, rounded lines and bombastic colors, while Jafar has several sharp angles and muted colors.)
Mulan is the story of a girl who goes into the army to save her father's life. While the movie is comedic much of time (and has a non-threatening dragon voiced by Eddie Murphy and a cute little cricket), the Big Bad Shan-yu is implied to kill vast numbers of people. The aftermath of his handiwork makes a Mood Whiplash from a song about getting a girl to seeing the most straightforward example of War Is Hell in a Disney movie. The scene with the destroyed village also has a subtle implication that the Infant Immortality was averted with the appearance of a doll without its owner. Further, of the Disney villains listed here, he's the one whose sidekicks are also scary, mostly competent, and definitely not wisecracking parrots.
Professor Ratigan of The Great Mouse Detective spends most of the film as the epitome of the Faux Affably Evil, Evil Is Hammy villain (this is helped by being voiced by Vincent Price, who is very obviously really enjoying himself), so it's easy to forget that he kidnaps frightened children and has no qualms about threatening them or getting them killed — a throwaway line in his Villain Song refers to "those widows and orphans you drowned". Then his temper gets pushed that little bit too far, and... HolyShit.
101 Dalmatians has Cruella DeVil — for all her campy vampiness, her basic goal is still to kill and skin a bunch of puppies to make them into fur coats.
Scar, from The Lion King. Simply put, he gets the honor of committing the first onscreen murder in a Disney film.
Beauty and the Beast has Gaston. While he starts out as a fairly comedic foil for Belle, as the movie goes on, he turns into one of the most realistic depictions of a possessive abuser ever shown in a kids' movie. By the time he's having Belle's father committed under false pretenses, leading a mob bent on murder to the castle, and stabbing the Beast immediately after the Beast saves his life, he's become one of Disney's most menacing villains.
The Fox and the Hound starts off as a cute dog/fox bonding story, and ends in a fight with an utterly terrifying bear.
In a (semi) Live-Action example, Judge Doom from Who Framed Roger Rabbit. The film initially seems like a classical family movie until we meet him. We discover that not only is he responsible for all the bad things that happen in the movie, but he's also the same psychopathic murderous toon who killed Eddie Valiant's brother long ago and he was planning the genocide of his own species to profit him.
Toy Story is a lighthearted series where the main conflict is usually within the heroes as opposed to external. Villains tend to be either Obliviously Evil or relatively harmless. Until Toy Story 3, that is, where we meet Lotso, a sadistic teddy bear overlord of a day care center who subjects new toys to being broken by toddlers, tortures, brainwashes, imprisons, and attempts to murder the heroes, and eventually leaves them to die in an incinerator AFTER THEY SAVE HIS LIFE!
Hopper in A Bug's Life is a ruthless tyrant who delights in the fear he instills in the ants, and was fully prepared to publically execute their queen to keep them compliant. He even admits to his minions that they don't even need the food the ants provide, implying his actions are motivated purely by sadism.
Charles Muntz in Up is a delusional and sociopathic murderer who kills anyone who he even thinksthreatens his discovery.
Kung Fu Panda 2 has Lord Shen, an evil peacock tyrant who is bent on destroying kung fu with heavy artillery, terrorized many innocent pigs and bunnies with his army of wolves, and he almost pushed the entire panda species (which includes Po) to the point of extinction! All of this is enough to make Tai Lung, the snow leopard villain of the first Kung Fu Panda film look like a scaredy cat. When Shen's right hand and the leader of the wolves objects to him opening fire on his own soldiers to get at the heroes, Shen responds with a daggerto his back, making it the first time in a Dreamworks movie a villain actually offs someone onscreen.
The Brave Little Toaster is a cute musical film about talking electrical appliances, but then we meet the Junkyard Magnet...
Also in the movie, there's the cyclops diver, who captures sea creatures and painfully kills them using the heat of a bright lamp, then sells the dried-out remains as knick-knacks (although whether or not he knows the fish are sapient and screaming is left as an exercise to the viewer).
Brave gives us a sweet mother-daughter bonding story...with a villain, Mor'du, that happens to be a red-eyed, twelve-foot-tall bear with a taste for human flesh. As well as plenty of scenes that could have come right out of a horror movies, such as Mor'du watching a young Merida in the forest, Merida going into a castle and having Mor'du sneak up behind her after she's learned his gruesome origin story, and the end fight, where absolutely nothing hurts him except a bear of similar size and a multiton rock.
Madagascar 3 follows a parade of colorful animals, some escaped form the New York zoo, others part of a circus. The villain, Chantelle DuBois, ostensibly an animal control officer, is out to murder the protagonist by any meansnecessary. Even after the escaped lion in question is safely contained in the zoo, she still tries to kill him (and an innocent sea lion!) and steal his corpse so she can add it to her collection of trophies.
The Iron Giant starts off looking basically like a funny, cute Wish Fulfillment story about a lonely young boy who befriends a giant alien robot while dodging a bumbling, ineffectual government agent... until said agent locks him in a shed and threatens to take him away from his mother if he doesn't tell him what he wants to know. Oh, and then chloroforms him.
Ice Age is one of the forerunners of the family-friendly CGI comedies. Its villain is Soto, a sabertooth tiger who wants to murder a human baby.
Rise of the Guardians is an animated adventure film focusing on a team of Santa Claus, The Sandman, The Easter Bunny, The Tooth Fairy, and Jack Frost that protects children. The villain is Pitch, the living embodiment of childrens' nightmares, who commands an army of monstrous shadows and murders one of the core team members in cold blood (he gets better) and in the finale is willing to kill an innocent child in order to boost his power.
Coraline is an animated fantasy film about the titular heroine who wishes her busy parents would pay more attention to her and is, for the most part, pretty lighthearted. The main villain is the Other Mother, AKA the Beldam, a villainous creature who lures children to the Other World with false gifts and love to feed on their Life Force. She assumes a more monstrous form as her plan unravels and it's heavily implied that Coraline is the latest in a long line of victims and possibly the first to escape her clutches.
The 1939 film version of The Wizard of Oz, unlike the book, portrays the Land of Oz as a Sugar Bowl, but the Wicked Witch of the West remains being just as mean (If not meaner) than her literary counterpart. Even though the movie is definitely not a horror film, by any stretch of the imagination, many serious film buffs still consider the Wicked Witch to be one of the scariest cinematic characters of all time.
And In Oz: The Great and Powerful, there is Evanora, The Wicked Witch of the East, who manipulates her formerly good sister Theodora, turning her into the Wicked Witch of the West.
Guardians of the Galaxy is generally pretty lighthearted and fun... that is, with the exception of Ronan the Accuser. Disgusted with the Kree for signing a peace treaty with Xandar to end the war that resulted in the loss of his father and grandfather, Ronan immediately separates himself from the rest of the Kree and doubles his efforts to find what Thanos had requested of him so that he will annihilate Xandar; once he realizes that that item is actually an Infinity Stone, he immediately ceases their partnership and vows to come after Thanos once he's done scouring Xandar clean of life. He's a genocidal maniac and brutal zealot who thinks that wiping out an entire planet as retribution for two deaths is a totally acceptable course of action, and his incredible cruelty towards enemy combatants and callousness when confronted with his actions further hammers home how truly loathsome the guy is.
Redwall; it seems like a happy fluffy world full of cuddly talking animals. Then you meet the villains, who made this the first book series to get its own Complete Monster page.
Tove Jansson's The Moomins take place in Moominvalley which is, at least at a very quick glance, somewhat of a saccharine world in the early novels and some of the adaptations. Then we are introduced to the Groke. The revelation in later stories that she's a Tortured Abomination rather than consciously evil may make her less, or even more, horrifying depending on your taste.
Even though Seinfeld is not exactly a cheerful show (it's actually quite cynical), Joey "Crazy Joe" Devola still adds a surprising dash of darkness to it.
An in-universe example appears on Star Trek: Voyager with the Show Within a ShowThe Adventures of Flotter, a series of fantasy holonovels for children. One of the title adventures involves a character called the Ogre of Fire, who shows-up, vaporizes the main character in front of the child's eyes, and then torches the setting to the ground.
Whoever designed The Adventures of Flotter was very twisted; some of the characters talked to Naomi Wildman (a child) about the ways he and his friends could kill Neelix. Right in front of him.
Yogoshimacritein - The true Big Bad in Engine Sentai Go-onger. Not only is he more evil than his son, but he's also a veryBad Boss, killing off his two minions once they double-cross him to help the Go-Ongers. He also has access to a device that deletes people from existence.
Kamen Rider Fourze—a High School version of Kamen Rider penned by the same guy who made Gurren Lagann—seems cheerful, right? Wrong. The monsters, known as Zodiarts, are actually fellow students—many of them having lots of psychological issues—alongside the teachers who actively are giving them the means to become evil. In fact, it has the most amount of monsters out of all the Kamen Rider Series with a total of at least eight that are trying to kill teenagers.
The Aquabats! Super Show! is a surreal children's show that runs on pure silly camp. Then in the season finale Space Monster M shows up murders superheroes before the team's very eyes, devastates a city, and vows to destroy the earth.
Once Upon a Time in Wonderland is notably Lighter and Softer than the series it spun off from. The Big Bad, however, is Jafar, bastard son of the Sultan of Agrabah, Evil Sorceror, and all-around monster. Every episode has him doing something despicable: torture, murder, attempted murder, manipulation, and turning his lover into his serpent staff. He also has a particularly dark backstory that features his equally horrible father attempting to drown him when he was a child among other things.
Kickin' It's Sensei Ty started out this way; in The Pilot he ordered a student to break Jack's leg. Let me restate that - he ordered a teenage martial artist to break another, younger one's leg in tournament play. He's gotten broader and sillier since.
Thunderbirds has the Hood, who regularly causes disasters that could potentially kill hundreds or thousands of people, just to force International Rescue into action so that he can try to copy their technology.
Kirby is in LOVE with this trope, being a Sugar Bowl with some really nasty major villains.
The most common recurring villain, Dark Matter, is an Eldritch Abomination who appears in a multitude of disturbing forms. These include the basic cycloptic dark ball with yellow dots on its back, or a cloaked knight appearing as the first form of Kirby Dream Land 2's True Final Boss, Miracle Matter, a 20 sided die that appears as the Final Boss of Kirby 64: The Crystal Shards, and Zero from Kirby's Dream Land 3, the boss of Dark Matter who cuts its own iris and bleeds as an attack, and later it rips its own iris out. It is reincarnated as 02 in Kirby 64 as the True Final Boss, a creepy angel thing with a blood-dripping eye.
From Kirby Super Star there is Marx, first appearing to be a cute jester-like creature balancing on a ball, he manipulates the Sun and Moon to fight and sends Kirby to stop them as part of a plan to wish for ultimate power. He is killed, but his grotesque soul appears as a Bonus Boss that terrifyingly screams when you defeat it.
Kirby Mass Attack has Necrodeus, the monster that split Kirby into ten pieces, and the Skull Gang, his minions. It doesn't help that his name translates to "Death/Corpse God".
Kirby: Canvas Curse has the lesser-known Drawcia Soul; the soul of a painting that came to life. Not only does it look and act like an Eldritch Abomination, but it has a high-pitched, warped and rather disturbing scream to go with its apperance.
Mother 3 has Porky Minch, who commits an array of disgustingly horrible acts,note Such as: killing your mother, killing your brother, resurrecting said brother and brainwashing him to be a right-hand-man, sending said right-hand-man to kill you, burning down the forest you used to play in, taking over your perfectly peaceful village, corrupting all the people you care about into selfish, pleasure-obsessed jerks, violently torturing a huge population of animals, and aspiring to kill everybody in the worldother than himself. Please note that "you" are a perfectly innocent 12-year-old boy. ultimately because he was bored.
Real Overlord Zenon in Disgaea 2: Cursed Memories. She's made even more horrifying in the infamous worst ending. And yet, thanks to the magic of reincarnation, she's also the hero's love interest.
Smithy in particular set the standards as the villain of the first Mario RPG. After traversing the Mushroom Kingdom which as to be expected is bright, colorful and full of wacky and strange enemies... you find the portal to Smithy's realm and find it a dark, gloomy, mist-covered factory full of machines and ghosts.
Antasma from Mario & Luigi: Dream Team was this to the cute and colorful Pi'illos in the game's backstory, looking like something out of a nightmare in contrast. And even though the game proper sees him get upstaged by Bowser as the main threat, he still looks pretty creepy compared to the other characters.
Luigi's enemy King Boo might count too, if you look into Luigi's Mansion close enough. The Portrait Ghosts (who are allied with him, apparently) are a family and servants, some of them children, and many of their biographies give them sympathetic backstories and suggest that they may have died in very unpleasant ways. One of them even befriends Luigi. Given that King Boo created the Mansion as a trap to lure Mario and his friends to their doom it is entirely possible that the Portrait Ghosts were Unwitting Pawns all along, putting King Boo on the same level as Dimentio in terms of what he's capable of.
Then Luigi's Mansion: Dark Moon happened, in which it's revealed that his defeat turned him into a complete and utter sociopath perfectly willing to do anything to make Luigi and Gadd suffer as much as possible, even attempting to destroy the fabric of the universe. He's not just as bad as Dimentio in what he's capable of doing. He's as bad as him in what he does.
Darkrai, the main villain of the Pokémon Mystery Dungeon series games. Prior to the second game's events, he steals artifacts responsible for the balance of the universe as an attempt to destroy both space and time and in the process, he makes one of the gods evil and crazy, then he wipes the hero(ine)'s memory clean and turns him/her into a Pokémon. Later, when this doesn't work, he decides that the easiest way to get rid of his aforementioned archnemesis is to make him/her commit suicide!
In the main series, the best example is probably Pokémon Platinum. The Sinnoh games are arguably among the cutest in the main series so far (because of the music, the many pre-evos, and in fact most of the new mons introduced that generation, notably) but the mascot legendaries are among the most powerful ever (at least in-story) and Platinum ups the ante with a sinister Ghost/Dragon Eldritch Abomination (that isn't a villain per se, but an antagonist) that lives in an appropriate Eldritch Location. The contrast with the rest of Sinnoh can be stunning. And it's awakened by the actions of the above-mentioned emotion-hating and omnicidal Cyrus.
Pokémon Black2 and White2 are right up there, too, with Team Plasma and the aforementioned Ghetsis actually freezing part of the continent using the power of Kyurem, a creature nearly as terrifying as Giratina. Furthermore, Ghetsis forces one of the other two dragons to merge with Kyurem to make it even stronger.
The series takes place in a dreamlike environment with mostly cute characters... but occasionally has genuinely creepy enemies. The Dark Passage level from the first game is rife with these as is Haunted Towers.
The Metropolis level from Spyro 2 is a rather jarring break in an otherwise cutesy game, with its psychotic cows in space suits who stare angrily and shoot you, as well as exploding pigs who come flying at you out of nowhere (and they will always hit you unless you kill them first). The robotic sharks in water levels are horrifying, especially when you try to go in there without a submarine (you are killed instantly). And also there are levels where plants can eat you. There are quite a few bosses who are pretty unnerving as well.
The Sorceress in 3, who steals all the baby dragon eggs because she wants to kill them and use their wings for an immortality spell. Yikes! No wonder her Dragon did a Heel-Face Turn after she found out! The most disturbing part is that she didn't need to kill the hatchlings, she just didn't want them squirming about while she cut them off. Scorch, the 3rd boss, is pretty damn creepy as well, being solely created for the purpose of brutally murdering the heroes. Granted the manner the Sorceress reveals her evil plan fails tobe thatterrifying at all...
The Sorceress: What did you think I was going to do with all those eggs? Put them in a zoo? (mook in the background giggles quietly)
Wario Land 3 has enemies and bosses typical of the series... and then there's Rudy the Clown, who turns this Up to Eleven via Interface Screw and sudden subversion of a core game mechanic. Not only is he a powerful demon◊ (blood-red teeth and Evil Laugh not shown) who becomes even more disturbing when he Turns Red, but he's the only thing in the game that can actually kill Wario, and the game auto-saves if he does. Fortunately, all this does is let you skip the cutscene before the fight next time, and most consider him an Anticlimax Boss once you know how to dodge his lethal attack.
LeChuck from the Monkey Island series can be truly threatening sometimes. And even when he's more humorous, his entire concept of being a demon zombie pirate is incredibly vile.
Rez the evil cyborg overlord from the Gex series. In addition to being incredibly creepy looking was downright Nightmare Fuel when you read between the lines. Judging from the fact that he has sentences like "NO HOPE" "30 DAYS IN THE COOLER FOR TALKING" "YOUR WORK IS THE REASON YOU LIVE" and "EMOTIONS ARE CRIMINAL" written throughout his lair it was heavily implied that he was using slave labor. Not to mention the sweatshop vibe the place gives off.
Lord Arktivus Brevon from Freedom Planet is an alien warlord who's as vile as they come, in what would otherwise be a lighthearted romp in the style of the early Sonic the Hedgehog games. You don't have to go further to learn of this than the game's opening sequence, in which he breaks into a palace with his army and beheads its king on-screen and in front of his son, who he promptly and painfully brainwashes to serve him. Whenever he shows up, expect things to get serious, and fast.
Much of the time, Suburban Knights has the same tone as the rest of the site; definitely not for children and sometimes resorting to Refuge in Audacity, but still comical and not taking danger very seriously. However, this doesn't hold true when Malachite — an apparent complete sociopath who murders multiple innocent people just for using technology — is on screen. While most of the site's villains are Played ForDark Comedy, Malachite is almost always Played for Drama.
Care Bears, of all franchises, tends to have this in spades, what with Professor Coldheart, the Spirit in the Book, Dark Heart, No-Heart and others all dedicated to the removal of any ability to feel emotion. Appropriately, Professor Coldheart has the (relatively) lightest/softest/most saccharine look, but the resemblance of his tactics' to pedophiles' could be said to make him simultaneously the creepiest.
The New Adventures of Winnie the Pooh episode "Cleanliness Is Next to Impossible": a creature named Crud (voiced by Jim Cummings using his Robotnik voice from the Sonic the Hedgehog SATAM show) imprisons Pooh, Piglet, and Tigger and then tries to force Christopher Robin to help him make the rest of the world dirty by saying "If you don't, YOU'LL NEVER SEE YOUR FRIENDS AGAIN!". Granted, by normal standards this hammy cartoon blob is not much worse or creepier than mostDisney Afternoonvillains, but he's much more so then you'd expect from one of Disney's lightest and softest universes.
The initial specials have Tirek, a demon-centaur who wanted to turn the ponies into an army of demonic dragons with his "Rainbow of Darkness", and Katrina, a catwoman sorceress who plotted to enslave the ponies into gathering ingredients for her Fantastic Drug of choice, "witchweed potion".
Squirk, a tyrannical sea monster who wanted to reclaim part of his undersea kingdom by flooding Dream Valley.
Crunch the Rock Dog, a huge dog made out of stone that hates all things soft, has the power to turn anything he touches to stone and turn normal rocks into sharp-toothed monsters to stalk his prey. The way he and his rock minions chased after the Bushwoolies, turning them to stone one by one, seems right out of a horror movie.
QueenChrysalis in "A Canterlot Wedding", whose modus operandi is to replace and impersonate individuals, draining their loved ones to increase her own power and put them under Mind Control, before leading her minions in a full scale invasion so they can feed as well and drain everyone. It's implied that Equestria isn't the first land she's done this to, and she's even worse in the IDW comics.
Him, one of the scariest (and most daring) villains on a Cartoon Network comedy ever; he even turned Townsville into a living hell on Earth when the girls accidentally traveled forward in time. But at least Him has comedic traits, which is more than can be said for...
Dick Hardly. He tricks the girls into giving him some Chemical X, and then starts making shoddy knock-off Powerpuff Girls to sell around the world and become rich. He has them made intentionally poorly, so that they fall apart and he can sell more of them, and when he sees a perfect Buttercup copy, he angrily orders it to be melted down for its excess Chemical X. When the girls go to his factory to stop him, he starts draining their Chemical X, nearly killing them. And when the Professor offers to become Dick's slave and make Chemical X for the rest of his life in exchange for the girls' safety, Dick laughs at him and says that he'll destroy the girls and keep the Professor as a slave.
Sideshow Bob from The Simpsons has always been distinctly darker than anybody else in a cast of hundreds. Especially prevalent in his third appearance, "Cape Feare", in which he forgoes evil plans and just tries to slice Bart to pieces with a machete, crouched and approaching with dark rings under his eyes. Perhaps to balance this out, Sideshow Bob episodes are also frequently Denser and Wackier, even in the show's earlier, more "down to earth" seasons. In "Cape Feare" alone, Sideshow Bobis driven through a cactus patch, walks through a pile of rakes and gets trampled by circus elephants. He later sings the entire score of H.M.S. Pinafore as a final wish to Bart before attempting to murder him (complete with makeshift props, costumes, an issue of Playbill with his picture on the cover, and a giant Union Flag unfurling behind him during the grand finale).
Cecil Terwilliger is definitely a Up to Eleven version of Sideshow Bob. He tried to kill two children and his own brother.
Mr. Burns, especially in the earlier seasons. Freudian Excuse aside, his Kick the Dog moments are much more frequent than those of other Simpsons villains. The few excuses he is given seem so disconnected from his evil, he is hated throughout Springfield, (Who Shot Mr. Burns has even Snake Jailbird apologizing for not being around to shoot him).
Father from Codename: Kids Next Door. A shadowy figure with control over fire, who brainwashed five children into thinking they were his/being evil? Add that to the fact that he is always beaten by the skin of everyone else's teeth and you've got a very threatening villain for such a harmless show.
And then once Father went through massive Villain Decay, The Movie gave us Grandfather, Father's father (and Numbuh Zero's), who possesses many of Father's abilities as well as the ability to turn all the people in the world into undead senior citizens.
Phineas and Ferb is a show that invokes Rousseau Was Right and usually has a Ineffectual Sympathetic Villain, which makes the presence of the unnamed Drill Sergeant Nasty in "Phineas and Ferb Get Busted" all the more surprising. He spends the entire episode coldly and sadistically pounding out any creativity and happiness from the duo to the point they essentially become mindless drones. He even dies in the end. He's also a literal nightmare, so the show can get away with this.
Then, the crossover with Marvel presented Red Skull. Given his history and what he does, his evil stands out A LOT, compared to the Drill Sergeant Nasty and Doodenshmirtz-2. His evil plan was to destroy the Tri-State Area, and he modified one of Doofenshmirtz's inventions to drain matter and living energy from other beings.
Teen Titans sometimes has this trope. The show itself is usually lighthearted, and most of the one-shot villains are comical (with a couple of notable exceptions)- but lets take a look at some of the Big Bads. Slade is a creepily emotionless diabolical mastermind who runs on blackmail, Mind Rape, Hannibal Lectures and Foe Yay, and delivers No Holds Barred Beatdowns to several characters in surprisingly vivid fashion. Then there's Trigon, who's Satan and wants to use the show's main Woobie, who's also his daughter, to bring about The End of the World as We Know It- and he actually succeeds in causing Hell on Earth for two episodes. Fun times. Both villains (as well as Brother Blood) were toned down a lot for the cartoon. For much of the '80s, the Teen Titans was one of DC's darkest books. The fact that they were able to make it a kids' show is a feat for the ages.
Adventure Time is more crapsaccharine than saccharine (though the characters inside don't seem to care), but some villains are a cut above the rest:
The Fight King, who tricked friend warriors into fighting his Gladiator Ghosts, and then eventually forced them to fight and kill each other for his own amusement. Just like The Lich, he is a completely serious villain without any comical trait.
Me-Mow threatens to kill Jake if he doesn't assassinate Wildberry Princess for her, and at one point injects him with half the poison. Once she's discovered she tries to blind Finn with a knife.
The Destiny Gang are a band of marauding thugs that terrorise and plunder a village, burn it down purely out of spite, then set Finn's house on fire while his family are still inside (including his infant sibling). The two-part episode in which they appear features The Lich and finally confirms that Ooo is set After the End, and they are still one of the darkest things about the episode.
Ricardio is not only a blood covered giant organ with a scary looking face and hideous biomechanical limbs, he's also the closest thing to a rapist they could get away with having in a kid's show.
Shockwave, who murdered Blurrin an incredibly horrifying manner, Wasp, being in a continuity where his insanity isn't played for laughs and is completely terrifying for it, and Lockdown, a freelance assassin Transformer who's caused Ratchet to have war flashbacks.
Lockdown's whole body is a Swiss-Army Weapon whose left arm and leg don't match his right. Why? He butchers other Transformers for their parts to increase his power, or just to keep as trophies.
Prometheus Black/Meltdown is a rare human example in the series. While the other human villains in Animated are deliberately used as filler and to exemplify the Decepticons as a greater threat, Meltdown manages to be geuinely depraved and terrifying. Case in point — in his second appearance, he was experimenting on humans to try and create human transformers (he'd already done at least two adult humans, one of them his former lawyer, and was planning to use 8-year-old Sari Sumdac as his next test subject).
The Night Master from Yin Yang Yo. While he still retains comedic features, he is a really dangerous and intimidating villain compared to the Ineffectual Sympathetic Villains in the show. It went so far that he was responsible for the Woo-Foo extinguish, killing all the Woo-Foo's knights, Master Yo being the only survivor.
Gargamel was only the Smurfs' most persistant enemy. They had ones that were far more dangerous, and some that were not laughable at all. Nemesis, a warlock who was introduced late in the series, was the best example. His goal was to gain immortality by stealing the Smurfs' Long Life Stone, and an accident in the past had made his face so hideous that most people couldn't bear to look at him. His skills in black magic were greater than Gargamel could ever fathom.
There was also Gargamel's godfather Lord Balthazar, a far more competant wizard. The show's Never Say "Die" policy was severly compromised in his first appearance, when he used a gun (he didn't refer to it as such, but it was clearly a blunderbuss of some sort) against the Smurfs, killing their pet duck. (He later got better, due to Swiss Army Tears.) Balthazar mellowed a great deal in future episodes where he really didn't really care about the smurfs at all, but his plots to predict the future often made him a dangerous threat.
Another example was the Wicked Witch Chlorhydris, who was so full of hate that she wanted to make the entire world feel the same way, eradicating everyone's ability to feel happiness and love. While such goals are not uncommon for villains in a series like this, Chlorhydris did some downright sadistic things in pursuit of it, like kidnapping the wood elf Laconia and using her wand to kill the flowing plants in the forest - not caring in the least that doing so was causing Laconia to die an agonizingly slow death as she felt their pain. (Unlike most villains in the series, Chlorhydris was given a backstory; apparently, she was once in love with a wizard who left her at the altar, and apparently, the heartbreak was enough for her to want to deny all of creation what she had once had.)
Some of the oldest Looney Tunes shorts had villains that made even Yosemite Sam look timid. The 1949 Porky Pig cartoon "Bye, Bye Bluebeard" had a Serial Killer (that's right, a serial killer) named Bluebeard who would likely have given most of today's children nightmares. (Forget the fact that he was hideous, stood 6' 11 tall, actually had a long, blue beard, and the most nightmarish Evil Laugh in Looney Tunes history, he nearly decapitated poor Porky using a homemade guillotine; Porky was saved when a mouse (who Porky had been chasing earlier, who decides to flip a coin to decide what to do) tricks Bluebeard into eating some bombs disguised as popovers, causing the villain to explode.
Dr. Blowhole in The Penguins of Madagascar. In his debut episode he planned on flooding the world, just because of all the embarassment humans put him through when he was a circus dolphin. And in his second appearance, he intentionally meant to drown Skipper when he gave him amnesia. And that, after his first appearance, some of the other episodes went through Darker and Edgier territories.
A Finnish Children's show called The Moomins stars a family of cute claymation hippos — occasionally visited by the Groke, some void/cold/death incarnation that can apparently kill things just by standing near them. It also moves like some kind of demon ghost.
Ed, Edd n Eddy has Eddy's brother. Sure, the show itself was a Sadist Show, but everything that happens to the Eds up until his appearance is played for laughs and could be considered lighthearted enough. Come the end of the movie, this guy manages to genuinely harm both his own brother and Edd, and he's been abusing the former for years. What all the typical bullies in the show witness him doing is horrific enough for them to redeem themselves and accept the Eds as their friends once and for all.
Dora the Explorer normally only has Swiper, but some of the Big Bads in the double-length specials qualify — especially the Witch from "Dora's Fairy Tale Adventure", who put Boots in a never ending sleep For the Evulz and was genuinely evil.
Meatman from the Camp Lazlo episode of the same name is much more intimidating and terrifying than you'd expect from a show like this.
Lazlo: Please, Meatman! I'm sorry I called you stinky, smelly, and stupid!
The original Ben 10 is often goofy with a Silver Age feeling, but some of the aliens monsters fought by the protagonists even as one-off threat were outright disturbing. Then there is Vilgax, an Evil Overlord who tried to cut off the protagonist's arm to get his watch, and Kevin 11, an Enfant Terrible with psychotic tendencies who wanted to kill thousands of people to gain money.
"Of Predators and Prey" reveal Malware, a psychopathic Galvanic Mechomorph who was shown to have murdered people of his species. He tried to crash a school bus to distract Ben, trying to murder a bunch of innocent kids. "Showdown" reveals that he ripped out and destroyed Ben's Feedback form for no other reason than to spite Ben. The event left Ben traumatized and is visibly afraid of Malware. As if that weren't bad enough, he then proceeds to blow up his own homeworld.
The Fairly Oddparents is a cheerful series whose antagonists have at comical features, or themselves are incompetent. Except for Miss Doombringer. Unlike Crocker, her desire to find Fairies isn't to prove people right or conquer the world, she's just Ax-Crazy and wants to tear the wings off of Fairies to mount on her wall!
The Destructinator from the episode "Wishology". An Omnicidal Maniac dedicated to the destruction of other worlds and willing to kill a 10 year old boy. He is so atrocious he was the first and only character in the series to be Killed Off for Real.
In-universe, Vicky is often seen as this by other characters.
The Old Crazy Farmer/Janitor from Beavis and Butt-Head. Although, probably played for laughs, he certainly is much more frightening and creepier villain than any other.
Jake's father ("Mad Dog" Morgendorffer) from Daria. Even to be a mentioned character, he is the only villain in the entire series that has sociopathic traits. Violent, impulsive and Domestic Abuser.
King of the Hill has Trip Larson from the Halloween episode "Pigmalion". Not only does he try and transform Luanne into his ideal woman, he tries to kill her with a pork processing machine. He is known widely as the most memorable and frightening villain that had the entire series. Before of "Pigmalion", no other villain tried to kill someone young in the cast of the show in a so horrible way.
Donbot from Futurama. While the other villains are very ridiculous and over-the-top, Donbot's attempts to kill the Planet Express crew are played entirely seriously.
Scooby-Doo! Mystery Incorporated is Darker and Edgier than previous Scooby Doo series, but is still child-friendly. Two of its villains are The Freak of Crystal Cove and Professor Pericles. The former blackmailed the original mystery gang into leaving town and took the baby of one of them hostage and raised it for 18 years, threatening to harm him if they ever came back. The latter murdered Ed Machine, and the Gang's friend Cassidy Williams and later experiments with genes to create a mutant army of cattle that cause wide property damage and killed at least 29 people. He later puts mutated cobra larvae into his former master's spine.
The Grand Finale sees the release of the Nibiru Entity from his Sealed Evil in a Can and makes Pericles and the Freak look tame in comparison. He kills Pericles by possessing him and mutating his body into a hideous Eldritch Abomination, then proceeds to eat Brad, Judy, and Mr. E alive. Not stopping there, he turns Crystal Cove into Hell on Earth and eats the entire town on screen while summoning an army of monstrous Mooks. All in all, he's the Scooby Doo verse version of Satan. He's also the only villain in the series to be Killed Off for Real, his demise erasing him from time and making it as if he'd never existed.
Similiar, The 13 Ghosts of Scooby-Doo has titular 13 Ghosts (sometimes called demons). While some of them are goofy, few are quite nasty. Maldor the Malevolent, first ghost they fought, was menancing dark sorcerer, attempted to kill the gang with magic, imprisoned and threatened a wizard to get magic wand that would let him conquer the world and trapped Daphne in magic sleep Scooby barerly managed to break. Time Slime was outright sadistic, even for ghosts' standards, and managed to terrify Scooby so much he got Heroic BSOD and only broke from it when Vincent showed him vision of the future in which Time Slime turned world into a postpocaliptic wasteland, corrutped Flim Flam and Scrappy and drove Shaggy and Daphne insane. Nicara is Femme Fatale, who makes wizards fall in love with her and then drains their magic powers and almost did that to Vincent. Rankor actually looks like classic demon and, in order to prove himself worthy joining group of ghost trying to destroy the world, turned Vincent into stone, attempted to kill the gang and then some plane passangers.
Dr. Robotnik gets this treatment in Sonic Sat AM, which was the Darker and Edgier continuity for Sonic the Hedgehog in its day. Admittedly, Mobius in this series is a Crapsaccharine World at best (cutesy talking animals... who are hiding from a relentless army of robots in a world that's growing increasingly poisonous and polluted), but he's the guy responsible for making it so crapsack, his favorite method of conquest is herding sentients into a machine that transforms them into helplessly obedient machine slaves, and he's so creepy even his main toady (who is also his nephew) is scared to death of him.
While Courage the Cowardly Dog is pretty creepy and no stranger to Nightmare Fuel, most of the villains have some sympathetic motive or backstory or are otherwise Laughably Evil. But there are some who can take villain level much, much further. In order of appearance:
Katz, arguably the Big Bad of the series and Courage's attitled Arch-Enemy is simply put, the most disturbing example of a sadistic, psychopathic Serial Killer played straight on a kid's show. Never Played for Laughs, his MO is to set up false businesses to lure victims, then murder them in brutal ways when he's done (Feeding them to spiders, turning them into appliances or candy, etc). And it's heavily implied that the family is the latest in a long line of victims and possibly the only ones to escape.
Benton Tarentella, one of the lesser known villains, is a Zombie director who was a Serial Killer when he was alive, murdering people with his partner while pretending to film them. When he died, he still continued his murderous work. His debut episode had him attempt to revive his partner so they could devour Muriel.
Mad Dog is a vicious gangster who regularly abused his girlfriend Bunny and implied to put her in prostitution. When Bunny's friend Kitty tried to get her away from him, he threatened her. This caused Bunny to assume all dogs were evil. Much like Katz, Mad Dog is played completely seriously and is basically a Domestic Abuser played horrifically straight on a kid's show.