The Lich of Adventure Time is this, as he manages to kill and possess Princess Bubblegum, and even after his defeat, he still manages to live on through a certain background character. Nevertheless, The Lich is not immune to slapstick comedy and being made a fool of, although he still has absolutely No Sense of Humor and its also worth noting that in the pitch of the show, it specifically mentions in bold dripping letters that "The Lich Kingnote His original name before being changed for being the same as that of an existing character from another work is not funny." After his return in the season 4 finale, he's still as frightening as ever. He appears in Finn's dream complete with a jump scare, is in possession of the Enchiridion, currently possessing Billy, a famous hero of Ooo, and then manages to trick Finn into giving what he wants. Even after being out of the spotlight for nearly two whole seasons, he still shows how Dangerously Genre Savvy he is through a manipulation of events. He didn't just possess Billy. He killed him and took his skin. In his appearance after that, he kills Prismo in cold blood and unleashes a prison full of ancient dangerous criminals, with intent to destroy the universe.
The Ice King is usually a Sitcom Arch-Nemesis, but when his backstory comes into play, he is mournfully one of the most realistic depictions of dementia on the show.
Lemongrab. Several episodes focused on him are pretty dark, and when you learn his backstory, it's really quite tragic, not to mention that many speculate that the murder of his own son made him even more insane.
Supreme Dog from Arthur is a rather dark villain for a show aimed at young children. He gave children candy bars that were designed to get them hooked, and since he refused to eat one when asked, it is rather implied that they contained rather nasty ingredients. Thankfully, he was eventually arrested and his business was shut down.
Bertram is actually a subversion. He's Laughably Evil, but he's the major threat to the universe in "The Big Bang Theory".
Sonja as well is one of these. She initially had the same kinks that Quagmire had, but she goes further in her perversions than Quagmire does. When he confronted her, she beats him up, and throws him into her car and intended to board a ship and make him her sex slave. And it's all played seriously.
Evil Stewie, a clone with all of Stewie's evil traits and none of his good ones, who goes around killing and maiming and generally causing all sorts of mayhem purely for the hell of it.
Both lampshaded and played straight in The Venture Bros. episode "Victor Echo November." When Phantom Limb gets in an argument with Harmless Villain The Monarch, he shows his superiority by calling for the immediate killing of the Venture family, whom the Monarch has ineffectually antagonized for the whole series. When the Guild henchmen prove to be much more dangerous than The Monarch's Mauve Shirts, Dr. Venture asks, "This is different, isn't it, Brock?" Brock replies, "Yeah, we might not win this one." Later on, the Monarch himself becomes much more threatening by Season 4. When the person he's after is not Rusty Venture, he can come off as downright scary.
The Web Creature from ReBoot. The thing itself only appeared in three episodes, all told, but that doesn't matter. The damage had been done. Megabyte himself is an example. Despite being there from day one, he inverts the typical Villain Decay of 90s animation. He goes from season one's daily nuisance, to season two's master manipulator, to actually having won in season three.
Though he was introduced in the very first episode, Slade didn't take center stage until the end of the first season, and the previously light and comedic storyline took a much darker turn. Though humor episodes were still very common later on, any time Slade's around things get dead serious very fast. Things get even darker with the introduction of Slade's master, Trigon, though they return to normal after both are defeated. Needless to say, this was a show that tended to dance a jig up and down the Sliding Scale of Seriousness Versus Silliness.
The Puppet King from the episode Switched was very creepy and tried to trap the Titans' souls in puppet versions of them so that he could destroy their spirits and control their bodies forever.
Mirage as well, while most of the villains Aladdin and his friends faced are typical cartoon-y bad guys. Her introduction begins by lighting a village on fire. She was very much Darker and Edgier compared to the other villains, with goals usually being aimed only at making Aladdin and the other heroes suffer, or just outright causing destruction For the Evulz. Her exploits have included kidnapping children and turning them into nocturnal monsters, transforming Jasmine slowly into a poisonous hybrid snake monster in order to destroy her and Aladdin's love, and finally to wipe out Agrabah's very existence with a monolith that permanently erases anything that falls under its shadow.
Season 1 has Nox. When most of the villains of the series are harmless, being slightly ridiculous or just not evil at all, Nox is one hell of a dramatic villain. He is eager to destroy any living things to get their primordial energy, including a baby that he stalked for ten years. And some flashbacks seems to indicate that he's responsible for the death of his own family, and ready to kill anyone/anything to bring them back to life. Altougth it might be a slight subversion, because he was introduced in the very first episode; the later villains were more light-hearted.
Season 2 is relatively light-hearted, since the true Big Bad isn't revealed until episode 20. The villains preceding him all have humorous elements that make them less serious, even Rushu. Qilby the Traitor however is a real piece of work. He wants to suck the World of Twelve dry of its wakfu for completely selfish and petty reasons, and unlike Nox he has no real redeeming qualities. Season 2 become a lot more serious when he stops pretending to be a nice guy.
Apocalypse from X-Men: Evolution. After he appeared, the series got less goofy and more serious, with more dramatic tension and more focus on stories about mutant persecution, less on high school drama. Apocalypse's ultimate genocidal plan really emphasized this.
Before Apocalypse, the series' main example was Magneto.
King Hiss in He-Man and the Masters of the Universe (2002). Shortly after being released, he defeats Skeletor and his entire army of evil warriors, before breaking into Castle Grayskull. Although temporarily defeated, he later returns and destroys the royal palace of Eternia.
Megatron of Transformers Animated is another semi-example like Slade and Rubilax. He was there from the beginning, but once he gets his body back, things get bad.
And then when Shockwave gets involved, things get worse. The biggest one in the series is Lockdown. He has no comedic traits, is only interested in getting paid and claiming trophies from his victims, and is often regarded as the most evil Transformer in this series. Infact, his debut episode Thrill Of The Hunt, establishes that the series is not as immature as the art style makes it out to be. Lockdown's actions also led to the dark and troubled pasts of both Ratchet and Prowl. What's worse is that his backstory, alternate mode, and blank rubsign obscuring his faction brand all seem to suggest he was a former Autobot.
Prometheus Black/Meltdown is one for the human supervillains of Animated; the other villains, like Angry Archer, Professor Princess, and the Headmaster are all very comical and very much played for laughs. Meltdown, however, is played as a legitimate threat to the Autobots and also engages in some pretty horrific genetic experimentation, turning unwilling subjects into horrible monsters.
Unicron, essentially the Transformers equivalent of Satan. Transformers: The Movie opens up with him destroying an entire planet full of life, helping setting up the tone for the first of the movie.
Transformers Prime is very much Darker and Edgier compared to earlier shows in the franchise, but its far more evil depiction of Megatron, snarkiness aside, still puts into their trope, with plans he gets involved with often extending beyond killing the Autobots to wiping out all life on Earth, along with a world of pain for anybody who tries to get in his way that isn't Optimus Prime. There are two more notable and recurring ones, the former being Soundwave who's almost always creeping other characters out, and the latter being Airachnid, who commits genocide for fun and is brutally cruel to the point that other Decepticons hate her.
Chase Young of Xiaolin Showdown was introduced as the Big Bad in the second season. In the first season, the villain had been Jack Spicer who's comically beaten once an episode. While he was partly taking orders from Wuya (an evil spirit with no physical form), she was also strictly comical, except in the Season One finale. Chase, however, was a strictly non-comical and threatening villain.
Wuya deserves special mention. Like Rubilax, her snarking makes her strictly comedic for the most part... Then she gets free and suddenly the laughing stopped.
Father brought about the first of many, many dark storylines. Also Chad, Cree, and Class President Mc Garfield are all rather intense former allies whose personal relationships with the main characters made most of their appearances pretty heavy stuff. However, they're not totally uncomedic, which is not the same for...
In The Grim Adventures of Billy & Mandys Halloween Special, there is Jack O' Lantern. While quite comedic, he is shown to be the only villain to outsmart Mandy by not falling for her trap and capturing her. He is only defeated when Irwin, in the most hillarious use of Deus ex Machina shows up and humiliates himself enough to destroy Jack's army.
The Freak of Crystal Cove AKA Mayor Jones is even worse then Pericles. His deeds involve: Chasing off the original Mystery inc. Kidnapping the son of two of their members as insurance to raise as his own, scarring Pericles and pinning Mystery Inc's dissapearance on him, and causing the dissolving of the present Mystery Inc. as Fred leaves to find his real parents, Daphne blames it on Velma for not figuring it out sooner, Shaggy gets shipped off to military school and Scooby gets sent to a farm. And all this from a villain on a Scooby Doo show.
The finale has a final one, though only for its two-part sequence: the Nibiru Entity a being whose evil has projected onto everyone, and is responsible for all the costumes, all the cruelty, and all the evil, including that of the previous two. Once freed, he kills Pericles, eats the original Mystery Incorporated, and eats all of Crystal Cove. His destruction raises this to a meta-level — as he was erased from the timeline, all the evil characters grew up to be good, and everyone's lives are for the better, bar Daphne's sisters.
Granny from the episode "Have You Seen This Snail?". She, unlike other recurring villains in the series, she contrasts absolutely comical traits, and the episode itself made things very serious. Later, she revels in the death of all the previous snails! (She seems to have eaten all of them, though this is uncertain; she certainly overfed them.)
Plankton manages to be one in The Movie after he successfully manages to steal the Krabby Patty Formula and almost get Mr. Krabs killed.
Mrs. Puff becomes one in the infamous Season 8 episode Demolition Doofus. In the episode, Mrs. Puff punctures her inflation sac thanks to her pupil SpongeBob's reckless driving. When she learned that she may never puff up again, she enters SpongeBob into a demolition derby and hoped that he would die in it. To her frustration, SpongeBob survived due to his reckless driving, and he becomes a champion of the demolition derby. She then gets into a large monster truck and tries to run him down herself. She chases his truck all the way to the Boating School, and she ends up destroying it. She's able to inflate back up again after this.
The original Ben 10 series had, for the most part, episodes that feel somewhat like Silver Age stories, with a usually comical feel to it. This rule doesn't apply to Vilgax and Ghostfreak. Vilgax pointedly showed more explicit hints to the first season's Story Arc and Grandpa Max's Hidden Depths. Ghostfreak started out as a rather scary alien in the Omnitrix, but later he broke free and became one of the most ruthless and terrifying villains in the series.
In that same vein, the Forever Knights in Ben 10: Ultimate Alien, combined with Took a Level in Badass. In the earlier series and several earlier episodes, they were pathetic mooks that got beaten easily and usually made Monty Python references. In the episode "the Purge" their founder, Old George returns, ends their Enemy Civil War and unites them as one faction to rid the world of aliens, and the excrement hits the cooling device.
While the fourth series Ben 10: Omniverse is Lighter and Softer than the two sequels; Khyber the Huntsman is not played for laughs at all. In fact, he's the first villain in Omniverse to fully defeat and capture Ben.
Malware, a villain who first appeared in the first episode and whose origins were explained in "Trouble Helix". His origin episode, while showcasing his Fatal Flaw (a particularly bad case of boasting and talking on and on), also shows that he has committed murder (though not on-screen; the flashback cuts off before it shows the gruesome details), though the rest of the episode showcases him as what just seems to be another villain, until "Of Predators and Prey" reveals that he's the Big Bad, and shows that him, Khyber, and Dr. Psychobos forcefully test the Nemetrix on Phil, with no amount of comedy appearing.
Him of The Powerpuff Girls, compared to the rest of the show's Ineffectual Sympathetic Villain cast, had a much creepier presence (even noted frequently by the cast and the narrator) and frequently supplied Mind Rape or other much deadlier tactics of bringing the girls to an end. Granted he also often supplied in Nightmare Retardant and did have the occasional bumbling role (he was Camp Gay after all) but he was still miles deadlier than most of the Rogues Gallery, especially was the villain of the episode, in which none of the scenes with Played for Laughsnote if he wasn't the villain, he was just as comical as the other villains. And then there's the episode "Speed Demon".
Dick Hardly from "Knock It Off", who tries to slowly kill the girls by slowly draining them of their Chemical X, even after Professor Utonium offered to become his slave for the rest of his life.
Mojo Jojo himself is this in The Movie, where he had a much more dark presence than any episode of the series. He deceives the Powerpuff Girls, and is probably responsible for a mass murder and mass destruction in the city at the climax.
The RowdyRuff Boys. Three boys that have powers equal to the girls with talents and abilities to match. Despite their achilles heel the first time around; their revival removes that heel at the cost of some personal side effects (Boomer becomes more of a ditz. Brick is twice as cruel, but his guerilla tactics are still strong. Finally, Butch's bloodlust has been ramped up way beyond buttercup's own).
The Gnome from the episode "See Me, Feel Me, Gnomey". While not as terrible as those mentioned above, is probably the most powerful villain that has appeared in the series, since it seems to be a greedy, Manipulative Bastard that he just wants to be the only villain, a massive hypocrite manipulating and controlling the masses. He is also responsible for killing all the recurring villains of the series. They did get better with the gnome's destruction.
Played with in The Dreamstone with Zordrak. While he appears in each episode dishing comical banter to his far lessthreatening minions, the Urpneys, he is a genuinely intimidating villain, and the odd time he has an active role in a plan it is usually a sign things are going to get a bit more serious.
Inverted in My Little Pony: Earlier villains (like Tirek) were rather terrifying, while later ones are extremely goofy and hilarious.
Garble and his gang from the season two episode "Dragon's Quest" would also count as this while they're also not as dark as the villains but they are based on real life gangs. Disrespecting Princess Celestia was bad enough but it gets worse when it turns out that they steal phoenix eggs and smash them they also steal phoenix chicks as well and probably eat them! They make the other jerks and bullies of this show look like saints in comparison at least the other bullies respect Celestia but these guys don't respect her at all, hell, bet they would even go far kill Celestia if they had found Ponyville! Move over, Babs Seed! Garble and his gang the worst bullies ever!
The CanterlotWedding has the Changeling Queen, Chrysalis, who plans to feed off of the love and magic of Princess Cadence's groom, Shining Armor, in order to enable her invading army to breach the magical Deflector Shield that Shining Armor cast over the capital city and seize control over all of Equestria. She gets even darker in the comic where she turns the Mane 6 against one another (although they get back together and she intended them to), and intends to kill Twilight after draining her magic, and have her changelings feast on her friends when their emotions peak. Not to mention she kills a luvcat in front of the Cutie Mark Crusaders ( whom she also intends to do away with).
King Sombra, the villain of the third season's premiere "The Crystal Empire," is the most evil antagonist yet seen on the show between the sheer scale of his atrocities and the fact that a selfish lust for power is apparently his only motivation for it all.note As mentioned, Nightmare Moon has a highly sympathetic backstory, while Discord and Chrysalis's crimes at least were, in part, a result of their very natures. Unlike earlier villains of his tier, his episode almost treats him less like a character than a disembodied force of hostility (hence his few lines of dialogue; he prefers monstrous roars instead), and in a first for this show, he's seemingly Killed Off for Real in the end. Naturally, outside of some tension-lightening comedic moments, the overall events of the episode are presented quite seriously even when compared to past two-parters.
Babs Seed, while not as dark as the other examples from the show is a much more realistic and scary portrayal of a bully than one would probably expect from the show including her excuse for her actions, especially jarring compared to the relatively harmless Diamond Tiara and Silver Spoon.
Lord Tirek from the Season 4 finale takes the cake out of all the previous Knights in the show, considering he's literally stealing everypony's destiny by robbing them of their magic and cutie marks. To hammer the point home, see Discord up there? Tirek managed to one-up Discord by emotionally breaking him, something no one thought was even possible considering that was Discord's schtick. Add that to the sheer damage he's willing to inflict to get what he wants, even blowing up Golden Oaks Library, Twilight's home.
Admiral Zhao, while no where near as dangerous or as much of an example of this as Azula, did come off as a greater genuine threat than Zuko in the first season, due to both resources and lacking any of the noble and heroic qualities that Zuko had.
Amon from the Sequel Series, The Legend of Korra. The couple of episodes before his first appearance were quite lighthearted. Once he showed up, the first season got darker and darker with each episode.
The most notable thing about Amon is that he's the only major villain in either of the two series who's never once Played for Laughs or the butt of jokes from other characters.
The second season adds another villain with that distinction: Vaatu, the dark spirit of chaos, a victory by whom would bring about the end of humanity. While he isn't able to act until the finale, his presence adds a level of menace never seen in either show before.
The Red Lotus from Season 3; a group of people that have abilities that are not normal by the universe's standards, their end goal is to "free" the world by destroying all established governments and states. They are also the first villains in both series to actually kill onscreen.
Kuvira from Season 4 is a notable aversion of this. While no less threatening than the other villains in the series, Season 4's considerably darker tone and subject matter makes her stand out less in terms of making the plot serious.
Even though he appeared in only one movie, Dark Danny, Danny Phantom's Bad Future version, made quite an impression as the most dangerous and psychotic villain in the entire series, even worse than Vlad Plasmius. Vlad himself served this role in the first season, though to nowhere near as great an extent. His first appearance marked the beginning of the show's main Story Arc, and subsequent episodes that featured him tended to be darker in tone. He was also the first villain to utterly curb-stomp Danny.
Darkseid and the armies of Apokolips in Superman: The Animated Series. While Superman wasn't a goofy show, being largely a good combination of silliness and seriousness, the eight episodes where Darkseid appears are much more serious that regular episodes. In "Apokolips... Now!! Part 2", Darkseid kills Dan Turpin, a major supporting character; and in "Legacy Parts 1 and 2", Superman is brainwashed by Darkseid to attack Earth and many other planets, killing who knows how many people. It culminates with a brutal brawl between Superman and Darkseid.
Justice League Unlimited had several end of season threats amping up how much darker things were. The last season had this from the beginning via Gorilla Grodd (himself a recurring Knight). What would top this? At the end of that season, Darkseid returns and sets out for revenge against the Earth. Not only does he set crust digging machines all over the world to cover the entire surface in boiling magma, he also brings a kryptonite knife to carve out Superman's heart as a war trophy.
Likewise, Amanda Waller, starting in Season 3 but becomes much more pronounced in Series 4. She masterminded the Cadmus Arc and the episodes dealing with Cadmus and their experiments were among the darkest of the entire show.
Justice League had a few even before it became Justice League Unlimited that never appeared there, yet still had a lasting impact:
First of all there's Vandal Savage, who was one of the League's most recurrent foes in the first two seasons, and arguably the most dangerous. In his first appearance, "The Savage Time", he changed history so that the Allies win the War and he's set up as the dictator of a totalitarian world government, based in the US; the League (sans Batman, who didn't have a Ripple-Effect-Proof Memory due to circumstance) spend the entire three-part Season One finale having to fix this, and the stakes are high. His second appearance in "Maid of Honour" isn't as dark, but remains serious as he marries Princess Audrey of Kaznia (after covertly paralysing her father with poison) and tries to seize the world using a space station that can initiate a Colony Drop on any part of the world he wishes. His final appearance is in "Hereafter, Part II'', where it's revealed that his latest plot to Take Over the World wiped out humanity and civilisation; this dark tale ironically had him as The Atoner in the Bad Future, and after helping Superman return to the past to Set Right What Once Went Wrong, the reformed future Savage is erased from the timelinecontent that he was able to redeem himself.
Finally, the Thanagarian army in Season Two finale "Starcrossed". after which Nothing Is the Same Anymore. Odd hints about Hawkgirl not being who she seems come together and we discover she is The Mole, sent as an advance agent to Earth, and her entire backstory was a lie; then it comes out that the Thanagarians are lying about protecting Earth from the Gordanians and have far darker motives, and by the end of Part I the Javelin is destroyed, the League captured and Hawkgirl has picked her side. What follows sees the original Watchtower destroyed in order to stop a device that would destroy the Earth, and while Shayera manages to redeem herself it leads to her becoming The Exile from Thanagar for her treachery, and her teammates are torn about whether they can trust her again; she ends up leaving to find atonement (her relationship with John Stewart greatly damaged and their Relationship Upgrade undone), and events set up Unlimited from there. What makes the Thanagarians so dark, besides their lasting impact on future storylines, is that unlike some villains they aren't one-dimensional at all - their commander, Hro Talak is a terrifying case of He Who Fights Monsters as he's ready to do anything to do anything to end the Gordanians including mass murder of an uninvolved world, and his scenes with Shayera when he learns she loves Green Lantern and not him are uncomfortably close to Domestic Abuse thanks to battle choreography; next to nothing involving Thanagar in the future is portrayed in an idealistic light from then on, including when some of them return in JLU.
Perhaps the series' oddest move was evolving Daffy Duck into one for Speedy Gonzales. Similar to the above examples, Daffy was still rather bumbling and comical, however he was often portrayed as Speedy's most competent foe compared to the rest of his completely ineffective Rogues Gallery, often putting Speedy and his friends in much more dire circumstances (eg. enslaving them or depriving them of water) and downplaying the former's Comically Invincible Hero streak.
Similarly while the Woody Woodpecker series was consistently comedic, most of Woody's earliest foes were incompetent Asshole Victims to Woody's constant heckling such as Wally Walrus. Buzz Buzzard however made his mark by being an outspokenly sleazy and malicious villain, his first appearance starting off with him conning Woody into a phony insurance policy and then attempting to kill him to claim the profits. Buzz was toned down in later shorts, but remained one of Woody's most belligerent foes.
Also happens in The Movie, with the twist that the Knight of Cerberus in the movie is actually an alternate universe version of the shows regular Harmless Villain Dr. Doofenschmirtz. He is far more competent and scarier than the regular Dr. Doof, has actually conquered his dimensions Tristate Area and is now a cruel dictator who uses an army of robots to keep the population under control, turned Perry the Platypus into his loyal cyborg henchman, and isn't afraid to try to kill the protagonists.
In The Penguins of Madagascar, Dr. Blowhole can be established as one since he tried to melt the ice in the world and flood it so that the humans would have to go through a ring of fire, and in his second appearance, he intentionally tried to drown Skipper when he gave him amnesia.
Miss Power from WordGirl. Magnitudes more powerful than every other villain and WordGirl herself, and much more intelligent. Pretends to be a hero and trains WordGirl while slowly corrupting her and the citizens. When WordGirl finds out she's being played, Miss Power simply beats her up and takes over anyway. And given the nature of her powers, she's pretty much the embodiment of bullying.
Lord Dregg of the 1987 cartoon. The fact that he plays his actions more seriously than Krang, the Shredder and his goons, who were all Laughably EvilHarmless Villains, definitely shows that this guy means business.
The first episode of those Red Sky seasons introduced Berserko, a rogue scientist from Dimension X, vying for revenge on Krang, and also cause trouble on Earth. He's far more serious than any of the other villains in the show, except Lord Dregg, and this is the episode when the show takes a Darker and Edgier turn.
The Shredder was made crueler and more brutal and competent in the 2003 cartoon. This was just a small change compared to his even more completely monstrous self in Turtles Forever. And so far he's been this in the 2012 series. Even with the show operated on Rule of Funny, none of the scenes with him were Played for Laughs. When the Turtles actually face off against him for the first time, they end up getting their shells handed to them; they only manage to escape because the Shredder was distracted by Xever and Bradford mutating. Following that, the show got darker with the other main villains the Kraang becoming far more of threat with the gradual reveal that their plan was to terraform the entire Earth to suit their needs. Once Dogpound becomes Rahzar, he's nobody's comic relief anymore.
Sideshow Bob from The Simpsons. While still rather slapstick prone and displaying humorous wit (being voiced by Kelsey Grammer and all) most of his appearances he attempts to kill Bart (sometimes the rest of the Simpsons family too, if they happen to be standing between him and Bart) or Krusty The Clown and his intents are (mostly) played seriously with episodes becoming more intense and dark when he appears. He even has his own creepy music soundtrack...
The series had few villains who have no funny quirks and are played seriously. Examples include the winemakers from "The Crepes Of Wrath", who treated Bart like a slave and nearly killed him by giving him antifreeze-laced wine, the Babysitter Bandit from "Some Enchanted Evening" (who tied up the kids and tried to rob the house) and Bart's kindergarten teacher from "Lisa's Sax" (whose treatment of Bart made him consider suicide when he was only five, and made him what he is today).
Frank Grimes is an interesting case. Although he's not completely vile (only a Jerkass), things turn very dark in his only episode where he appears, "Homer's Enemy". For many fans, it's one of the darkest episodes of the series.
Wallace & Gromit: Piella. She murders twelve bakers, and plans on making Wallace her thirteenth. This was because she hated bakers.
While the show on a whole is lighter than previous continuities, Ultimate Spider-Man's version of Venom is, half the time, not played for laughs and there are less Imagine Spots whenever he manages to make an appearance. Similarly, his creator, Doctor Octopus, while hardly ever seen outside of his lab, also appears to have no humorous quirks and if he's in an episode, the episode has a likeliness of taking itself seriously.
And when Norman Osborn becomes the Green Goblin, things really get dark.
Courage the Cowardly Dog has Mad Dog. He abuses Bunny to the point where he buries her up to her neck in dirt when she tried to escape, he tried to drive her and Courage down with his car, and most importantly, he somehow caused Kitty to be convinced that all dogs were evil. And that, like Katz, he's played dead seriously.
Katz himself shouldn't be overlooked as well. Whereas the general series dealt with Courage battling monsters and whatnot, at least they had some light-hearted tones in those episodes. Katz starkly contrasts these themes as he's essentially an Ax-CrazySerial Killer played completely, horrifyingly, and competently straight. Courage usually struggles in the episodes he's in, nearly getting killed twice.
Freaky Fred's episode, while still quite funny, is a lot creepier than the average Courage episode. And that's saying something!
The Evil Vet as well, who sent Courage's parents into space.
Tigerhawk, when his shell was possessed by the Vok. His arrival was directly responsible for throwing Beast Wars into the endgame phase and the Nemesis two-parter that followed contained some of the bleakest moments in the series.
The second season of Hero 108 has Twin Masters, an Omnicidal Maniac and embodiment of Chaotic Evil determined to destroy all life in Hidden Kingdom. Their introduction take the show from lighthearted to a more serious action show.
While the other villains are comical and overly arrogant, Taurus Bulba is a crime boss of the Magnificent Bastard category who rarely acts comical or over-the-top. Not only did he kill Gosalyn's grandfather, but he also tried to kill her onscreen, just to blackmail Darkwing Duck for a passcode. The best part is that he's the very first villain to ever appear in the show.
Then there's Darkwarrior Duck, who's an alternative futuristic version of Darkwing Duck who has gone insane and overzealous on crime, and appearently even killed Negaduck at some time just to prove to everyone who was in charge.
Negaduck himself, while comedic, was also quite frightening, some of his plans involved actual murder.
TRON: Uprising has Cyrus. While TRON: Uprising was already much Darker and Edgier than most other Disney animated shows, it becomes even more so when he shows up.
He comes across as friendly and seems to be a protagonist (albeit a creepy one, what with his face...tatoos), until he reveals his plan to blow up the entire Grid.
Later on he forces the Renegade to make a Sadistic Choice in an attempt to ruin his reputation, and it works.
Trent Boyett from South Park belongs to this trope, he played himself seriously all the time in the episode "Pre-School".
The Super Adventure Club from the episode "The Return of Chef", who brainwash Chef and turn him into a pedophile, among other things, which eventually leads to Chef's death. The episode on whole is darker (and more bitter) than most South Park episodes.
Grandma Stoch, despite the absurdity of a grandmother acting like a schoolyard bully, is still rather disturbing, especially when she buries a fork in Butters. In the only episode where she antagonizes (Butterballs), the issue of bullying is played very seriously for Butters.
Sheila Broflovski in the The Movie is one of the few antagonists of the series that has been played seriously in a very short period, where her Moral Guardian anticts instigates a Canadian American War, and attempts (and succeeds) to execute Terrence and Phillip.
He can be Played for Laughs all the time, but Cartman is played much more seriously in the "Coon & Friends" trilogy, where he tames Cthuhlu into destroying things and people he doesn't like.
Nothing tops Cartman in "Scott Tenorman must Die." After several comical failures, Cartman succeeds in his revenge against Scott by getting him to unwittingly eat his won parents. Cartman then proceeds to lick up Scott's tears. Even Stan and Kyle are mortified.
But still, Tom's nothing compared with Jake's father ("Mad Dog" Morgendorffer). Although he never made an appearance in the series (he's confirmed to have died), he's probably the worst of all jerks in the series, starting because he mistreated his son, didn't care what happened to him, and didn't accept it as he should.
Eddy's Brother from Ed, Edd n Eddy's Big Picture Show. Considering that he is the only villain in the entire series who has dedicated all his life to physically assaulting children, starting with his own brother Eddy. His abuse on Eddy is still displayed in a cartoony manner but it the trauma is played in a poignant light and is probably the single most serious scene in the entire series.
Leanne Platter. The whole reason Luanne lives with her aunt and uncle is because her mom stabbed her dad with a fork. Only appeared on screen in one episode where she gets released from prison, but it's clear she hasn't changed a bit.
Debbie Grund qualifies, girl likes seducing her bosses and, when Buck gets in trouble with his wife, he ends up losing his job, leading Hank to become the new manager. She tries to seduce Hank, and threatens to tell Peggy that they had sex. She also plans on killing Buck when he gets back together with his wife, but, due to poor thinking, she ends up killing herself.
Trip Larson from Pigmalion. He is presented as a normal guy, but as time goes on, he shows deeper signs of dementia, such as keeping a pig in his mansion and having Luanne dress as the woman on his company's logo. He dresses as a pig and claims that he want Luanne to marry a boy who resembles the farmer on the logo and that they could live as a family based on the logo (with Trip as the pig). She naturally and sanely refuses, but Trip chases her into a slaughter house, and when the machines are activated, he attempts to pull Luanne with him so they can become the very meat they sell to the public. Is it a wonder that he gets killed in the one episode he appears? Rather tragically, he got an electrical shock right to his brain during the climax, after which he comments that the voices in his head have stopped and he has no idea where he is or why he's wearing a pig costume... Mere seconds before his death.
There is also Wes Archer a death row convict who's in the slammer for "accidently" killing a friend of his, who uses Peggy's trust as a teacher to get her to unwittingly smuggle cocaine in hour glasses into prison. His plan gets uncovered, and he tries to pass the blame onto Peggy, but the evidence falls flat, so he attempts to attack Peggy on the spot.
The episodes with Verminous Skumm as the primary villain tend to be Darker and Edgier than the rest of the series. He's one of the only villains who specifically wants to hurt and kill people, not the environment.
Zarm, Spirit of War and Destruction, began as The Corrupter, turned the Eco-Villians into a dangerous Legion of Doom who ruined the world and nearly killed Gaia twice.
Armondo Guitierrez has shades of this role in the early episodes of Freakazoid!. Most of the villains were primarily sketch-comedy caricatures, providing laughs first and conflict second, but the cliffhanger ending of "The Chip", where Guitierrez has Dexter tied to a chair and orders a man with a gun to kill him is played completely straight. In his second appearance, he returns as Freakazoid's fully-realized Evil Counterpart and only loses by a fluke.
The character still has a bit of comedy in him; in his first appearance he tends to unintentionally quoteKhan Noonien Singh, while in the second he gained Freakazoid-like wackiness along with his powers, in particular flipping out whenever Freak calls him a weenie ("DON'T SAY THE WEENIE WORD!")
While Avengers Assemble may not be as intense as The Avengers: Earth's Mightiest Heroes, it has a rather dark villain in Hyperion, a Knight Templar alien "protector", whose idea to eliminate crimes and help people is essentialy enslave everyone and have them submit to his ideal, but if somebody doesn't agree with his methods, then he considers you to be a part of a problem. He also has no problems with attacking children and it's revealed that he had enslaved his entire home planet and later destroyed it, simply because the people refused to submit to his totalitarian rule. Aside from one moment where he's comically deafened by Doctor Doom, he's been played dead seriously. Oh, and now he's part of the Cabal.
Dracula also qualifies, as his debut episode plays out a lot like a horror film (not to mention that he turned Black Widow into a vampire and nearly killed her, then drank the Hulk's blood and only lost because the gamma radiation turned out to be poisonous to him).
The Red Skull isn't a tiny bit friendlier than he was in EMH, either. He starts out as the Big Bad from the word go, but when he kicks his plans into high gear, that's when the show itself does the same.
Barry Dylan in Archer became this over time. At first he was simply another secret agent Archer didn't get along with, but after he became a cyborg and became mentally unstable, he killed Archer's fiancée, Katya. When Katya herself was resurrected as a cyborg, he attempts to kill her again, but then just steals her from Archer. He also murdered his boss Nikolai Jakov, simply to spite Archer, and became the head of KGB in Jakov's place. He was eventually stranded on the space station Horizon by Cyril, but later took over the space station and then he kills the crew. He eventually returns to Earth, but in the interim, Katya herself has taken over his Knight of Cerberus status by taking over the KGB herself and keeping Barry on a proverbial leash.
The Avengers: Earth's Mightiest Heroes would often slide on how serious its villains got. The most serious were likely the Skrulls, their story arc, the longest in the series, prompted massive Paranoia Fuel and their manipulations nearly succeeded in breaking up the Avengers. Outside of them, the biggest example is Surter. While he never got the chance to act as a direct antagonist, the episodes that merely dealt with the aftermath of his actions showed he laid waste to the whole dwarven realm, and to reforge his giant sword, he destroyed the star of an inhabited solar system.
On a more mundane level, the Red Skull is easily the most vile villain in the show, in spite of, or in part due to the fact that he is still a mere human (for a measure of "mere").
Surprisingly enough, Mr. Bogus actually shows one in the form of Bogus's Evil Counterpart, Baddus. Introduced in the second season premiere episode "Computer Intruder", this mean, green, more gremlin-like version of Bogus will often show up, depending on the tone of the episode. Baddus was introduced to indicate that while Bogus is a goodhearted gremlin, Baddus is actually the opposite, striving to make things miserable for Bogus and/or the denizens of Bogusland.
The short-lived animated series Family Dog was mostly a lighthearted series about a dog and the dysfunctional family he lived with, but the episode "Dog Days of Summer" introduced a trio of callous teens and their vicious dog that nearly killed the titular family dog.
Invader Zim has Tak, whose plan to fill the Earth's core with snacks for the The Almighty Tallest could only be stopped by the main characters working together.
The Boondocks fourth season gives us Ed Wuncler Jr., who's sociopathic antics are played realisticly, who keeps the Freeman family in his million dollar debt and his plans to help them only digs them deeper. Robert ends up having to literally sign up for slavery and later have to work in a slavery themed park called Freedom Land, along with others in his debt was slaves. He later attempts to cut of Huey's foot for defying him.
Serpentor from the 1980s G.I. Joe series is a debatable case. In his debut appearance, he proves to be a more ruthless leader than Cobra Commander and nearly conquers the United States in a single day. However, despite being a more effectual Big Bad than Cobra Commander, the tone of the series doesn't really get darker. The Movie, on the other hand...
Gideon Charles Gleeful starts out as some brat with a crush on Mabel. Then he tries to cut off Dipper's tongue for "getting in his way". Then he summons a demon, and nearly succeeds in taking over the Mystery Shack.
Preston Northwest. Despite lacking supernatural powers, he still proves to be one vile man underneath his reputable image, mentally abusing his own daughter with Pavlov-style conditioning, and willing to let his party guests die due to a curse inflicted on his family, all to selfishly maintain his public image.