The Earl of Lemongrab from Adventure Time goes COMPLETELY BATSHIT CRAZY in the episode "You Made Me!", and ends up electrocuting three young children and a 14-year-old boy, and assaulting a baby. His more malicious side was hinted at in an unused storyboard for "Too Young," in which he screams at a candy child and sends him to the dungeon for no reason, making the kid cry. This aspect of his character was not confirmed until "You Made Me!".
The Flame King ordered one of his minions to turf out Flame Princess when she was a baby and leave her to die. Fortunately, the minion couldn't go through with it.
He's also made a few attempts to murder him. He was talked out of it the first time by his wife and the second time Zuko barely blocked his attempt in time and ran for it.
TheBoulder once felt conflicted about attacking a young, blind girl. The Boulder soon overcame his conflicted feelings and tried to bury her in a Rockalanche! The Boulder got completely trashed in the ensuing fight. Then again, this section is a parody of the WWF and The Boulder seems to know Toph well enough later in the show, it's quite possible all of this was just a play for the audience.
Katara's mom Kya knew that Fire Nation soldiers would harm and capture whoever the last waterbender in their tribe was, regardless of age, which is why she gave herself in, and not her daughter. 'Harm' in this case actually meant 'kill'.
This definitely be applied to Sozin. He ordered the deaths of Airbending children. Who were raised to be pacifists. All of them.
Koh the Face-Stealer was quite delighted to see Aang. It had been some time since he had taken the face of a child.
The Kangaroo Court in "Avatar Day" had no qualms about boiling Aang, a twelve-year-old boy, in oil.
In the sequel, Tenzin's three kids are under 10, but this doesn't mean they're spared of being attacked or being this close to being de-bended by the Equalists. Since they're Airbenders like their dad, they do their best to fight back.
In Season 2, Korra's Uncle Unalaqups it to eleven and threatens to destroy Jinora's soul if Korra doesn't open the northern spirit portal for him. Despite Korra's compliance, he sends Jinora to the Avatar's version of Hell, making Unalaq one of the worst examples of this trope in a children's show.
In Season 3, the Dai Li show up again, unlike the average earth kingdom guards, who find Jinora and just scold her, they're willing to engage children with a lot more force the air benders forcibly conscripted, are frequently hit with earth discs to train them, and Kai is taken down with a barrage of them when he gets uppity.
And now, we have the Red Lotus threatening to kill everyone at the Northern Air Temple. In fact, P'Li actually shoots Kai out of the air, leaving it briefly ambiguous as to whether or not the latter even survives. (He does.)
The main villain in Ballerina doesn't seem to have any qualms against killing a child, even bystanders, first by hitting a boy on the head with a heavy metal wrench, then by trying to push a girl off a statue to make her fall to her death.
In "The Underdwellers". The Sewer King is exploiting and abusing children. Batman finds out and is less than thrilled. For just a minute, the viewer wonders about that train...
The New Batman Adventures has the new Robin meeting Two Face -who says he'll happily twist his neck.
The Joker displays this at first in the episode "Be A Clown", where he doesn't seem to care one way or the other if a party full of children gets blown up at the end of the first act; but in the Return of the Joker movie he brainwashes Robin through horrific psychological and physical torture.
In one episode of The Batman, the Penguin acquires two statues capable of focusing light into a death ray capable of destroying buildings; when Batman finds him, he threatens to use it on Gotham Children's Hospital.
One episode has Joker masquerading as Batman, the catch being that the "crimes" he stops are incredibly minor and he stops them by poisoning them with Joker Gas. One such scenario has him attempting to poison two elementary school-aged girls for drawing on the sidewalk.
A later episode has Joker recruiting a Kid Sidekick and then attempting to throw him in a vat of acid.
Considering Ben 10 stars a child superhero it would be pretty boring if this trope wasn't in effect.
XANA of Code Lyoko may be a computer virus and therefore not have human emotions but the episode "Ghost Channel" showed us that he enjoys all of the suffering he causes and the Warriors, his main adversaries, are all in the 12 to 14 age range with some of their schoolmates that got targeted being even younger. And some of the ways he's tried to get rid of the Warriors would have been rather messy, including the incident in "Ultimatum" where he not only imprisons hostages Odd and Yumi in a freezer warehouse (which is clearly terrible for their health) but fully intends on killing them if he doesn't get what he wants with it being heavily implied he planned to electrocute them to death and force Yumi to watch him kill Odd since she was so weak at that point she could barely stand let alone fight.
Not only does Ming never exclude Kshin from his various attempts to kill the Defenders (except by default if Kshin is absent from the scene in question) he directly targets the boy on more than one occasion.
In the final installment of the "Book of Enigmas" arc, Kronos is prepared to reduce Kshin to ashes in order to get his hands on the Book.
Subverted in an episode of Duck Dodgers. Martian Commander X-2 threatens grievous harm to a baby, but the instant said baby begins crying, he reassures the child that it is merely an empty threat and that he would never carry it out.
The villains of DuckTales (1987) had no scruples about trying to hurt or kill the show's kids, though they seldom actually got a chance to take it too far before the kids escaped or the adult heroes intervened. Specific examples include:
"Armstrong": When Louie charges him for melting the tires on the boys' bikes, Armstrong fires a laser at him.
"Where No Duck Has Gone Before": Alien overlord Bulvan threatens to mulch (literally, because the Kronks use "inferior beings" for fertilizer) the nephews and Doofus, and when he catches them trying to get away, he says he'll have them "stuffed."
"The Money Vanishes": The Beagle Boys intend to use Gyro's transporter ray on the nephews and float them off the face of the earth. However, the triplets get ahold of the ray first.
"The Land of Tra La La": The leader of Tra La La almost shoots Huey, Dewey, and Louie because of the chaos Fenton caused by introducing money to the village.
"The Golden Goose": The Beagle Boys turn the triplets to gold when they interrupt their attempt to steal Scrooge's latest treasure (which turns things to gold). They get punished when the artifact almost causes an apocalypse and they're some of the first to get transformed.
Denzel Crocker in particular. There are several examples, but the best one is at the climax of Abra Catastrophe when he was going to destroy Timmy Turner (Waste in Timmy's words) after the boy surrendered to him.
Implied in "Dream Goat!", when the citizens run after Timmy, Timmy makes comments on how his life would be cut short.
Family Guy: The flanderized Peter Griffin from the later seasons frequently attacks and occasionally murders people, and children are no exception. He punched out a child because he felt he had to hit someone, blew up a children's hospital (although that was an accident, but still), killed his own infant son Peter Jr. when he couldn't get him to stop crying, and threw his toddler son Stewie (who was in a coma with heavily infected wounds) under his wife's car so it would look like an accident.
In one episode, a clean-cut teen-aged boy fires a gunshot and claims his 2-year-old brother accidentally shot himself ... all because Meg asked him to the dance!
Another memorable segment saw Peter use Lucy Van Pelt (from the "Peanuts'' comic strips) as a punching bag after he grew tired of her picking on Charlie Brown.
The Chew Toy, Conrado, is only 9 years old, meaning that he often gets hurt by many characters, including adults. His teacher Cudi (who is female) has hit his head with a ruler and threatened him with a gun to force him back to class. He also gets hit with a baton by a police officer and has gotten punched by several adults in an episode, to the point he was hospitalized.
In "Sequestro", 34-year old Popoto shoots his child friends and kills them because they wanted his family's money. Interestingly, Conrado was not a victim in this occasion.
Futurama: "Parents, have you ever just tried turning the TV off, sitting down with your kids, and hitting them?"
Many of the various oddities in Gravity Falls don't seem to have a problem with harming or possibly killing Mabel and Dipper. Bill Cipher especially goes out of his way to try and kill or harm the two if the need arises (or he feels like being a dick), and vaporized Time Baby when the latter tried to stop his Take Over the World scheme.
Invader Zim: Zim and Dib may be the same height, but Zim is an adult Irken who underwent years of military training before coming to Earth. Dib, on the other hand, is in elementary school. Even though he's a science prodigy with access to his father's equipment, he is by no means Zim's equal — but this doesn't stop Zim from trying to destroy him. Tak's ship spells out the differences between the two in the second issue of the comic:
Taks Ship: Youre going after Zim. An Irken Invader with untold decades of military training and a history of violence and mayhem. You dont know where hes going or what he plans to do. And you are a feeble, unarmed human in a stolen ship that you have no idea how to use. When you catch Zim. You are going to... what exactly?
Dib: Well... stop him.
Taks Ship: Right then. Tracking Zims garbage signature for the earthbaby with no plan.
"Ballot Box Bunny": Humorously invoked and parodied in this election politics satire, where Bugs Bunny tries to one-up rival Yosemite Sam by dressing as a baby and, while Sam kisses all the babies, screams out that "He bit my widdle nose! The bad man bit my widdle nose" ... leading to a bunch of old ladies letting Sam have it.
"Honey's Money," another Yosemite Sam short where he really does it, frustrated at having to care for an innocent but dim-witted hulking oaf named Wentworth — at his ugly nag of a wife's insistence — tries to kill him off at least twice. First, Sam throws a ball into a busy four-lane highway to have Wentworth retrieve it, but after a round the wife puts a stop to it ... but only after making Sam go play fetch in the street! Next, Sam fills the park swimming pool full of hungry alligators; Wentworth jumps in with such a huge splash that the force causes the 'gators to be thrown onto Sam, who is still waiting in the truck.
"Pappy's Puppy," involving Sylvester and a bulldog (named Butch in this short), who has just become a father. When the baby bulldog attacks Sylvester — thinking at first his nose to be a ball he had let get away, and then realizing that he had just been trained to antagonize cats — Sylvester tries a number of tricks to off the bothersome little pup. These include placing him under a tin can, swatting the kid as he plays with his tail and playing fetch using a busy street as the park, which were harmless compared to the final two attempts to actually kill the baby bulldog outright: trapping him in a doghouse with a lighted stick of dynamite, and then rigging a booby trap where a bone is attached to a shotgun trigger. Each time, of course, Butch comes to save his son and force puddy to take the worst of everything.
Pretty much every villain from The Mighty Heroes had no problem with harming Diaper Man in spite of him being a baby.
Although his exact age is never given, Mighty Max is obviously a preteen boy. Not only are his enemies not afraid to attack him, most of them specifically want to kill him in the most horrible way they can think of, and they're not afraid to say so.
Hawk Moth of Miraculous Ladybug not only would hurt children, but brainwash them as well. Instead of fighting the heroes on his own, he finds normal people who are feeling negative emotions and turns them into supervillains under his command to do his bidding. Not only does he always tries to kill the main two teenage heroes Ladybug and Chat Noir, he has no problem using teenagers, children, and even a baby as his brainwashed servants and sending them to fight the heroes. Those servants are often tasked to cause wanton destruction and target everyone including children.
The New Adventures of Superman: In "The Wisp of Wickedness", the first person possessed by the wisp attempts to drive his car through a playground, and the second attempts to drop a school bus into a furnace. Fortunately, Superman is on hand to save the day.
The Powerpuff Girls: As the main characters are child superheroes, and all of the villains they face know it, every villain on the show is willing to attack and harm kids. The one-shot villain Dick Hardly takes it a step further than the others, though, as he almost successfully kills the girls (and all in front of Professor Utonium, to boot).
Adult-on-child violence is rare ... except for instances where Homer chokes Bart (usually when Bart says something he shouldn't and it gets Homer in trouble). The strangulation issue with Homer is the most common instance of this trope, but Bart Simpson in general seems to have this effect on many adults in the show.
The villains aren't exactly above hurting children, especially Bart. Sideshow Bob has repeatedly attempted to kill Bart. Fat Tony has on several occasions had his crooks threaten Bart with violence up to and including murder. Burns threatens Bart with a gun prior to attempting to drown him as seen on the page picture, and that's apart from repeatedly letting The Hounds loose on him. Snake Jailbird has tried to run over Bart with his car, but as always, Bart's Plot Armor makes sure that the alley he is standing in is too narrow for Snake's car to pass.
From "The Great Wife Hope" there's Chet Englebrit, commissioner of the "Ultimate Fighting League." During a fight with Marge, Bart comes up to him to challenge him. His response is, "Heck, I'll fight anyone. Except a man my own size". Seeing Bart about to get hurt is what puts Marge on the edge.
Gargamel of The Smurfs would even hurt Baby Smurf, which sets off Smurfette's Mama Bear instinct when she was turned back into her Evil Self by the wizard who created her.
General Grievous shows on multiple occasions that he delights in killing Jedi at any age, and fantasizes about slaughtering the younglings in the temple on Coruscant. In "Duel of the Droids" he tries to strangle Ahsoka to death while threatening her with her own lightsaber and in "Lair of Grievous" Kit Fisto and Nahdar Vebb discover among the trophies he keeps from his victims is a display table full of padawan braids.
In the episode "Children of the Force", Darth Sidious is perfectly fine with performing potentially lethal experiments on infants. Cad Bane, who kidnapped the infants for Sidious, didn't really care what happened to them, so long as he was paid.
In "The Academy" Prime Minister Almec threatens to kill Satine's nephew if she doesn't give in to his demands.
In "Revenge", Darth Maul butchered dozens of innocent people, including several young children, to attract Obi-Wan's attention.
In "Death Trap", Aurra Sing displays no compunctions about the idea of abandoning an escape pod full of clone children to die in space - saving only Boba - because the kids are witnesses to their crime. She even seems faintly amused by it.
Star Wars Rebels: The Inquisitors take sadistic glee in hunting down force sensitive children to kill them, and take infants to Darth Sidious with the implication being that he never gave up on those horrific experiments he was doing during the Clone Wars. Vader also hunts down force sensitives of all ages, but does not express anything resembling glee, rather anger at the universe at large and pride in his own abilities and appears to kill those who don't have training he can take advantage of by turning them into Inquisitors.
The episode "Stanley's Cup" plays this trope straight, with the Detroit Red Wings brutally beating the kindergarten hockey team to a bloody pulp.
From "Terrance & Phillip: Behind the Blow", the Earth Day Brainwashing Committee (who might be the episode's antagonists) aren't above chopping off Kenny's limbs.
The infamous ending to "Jared Has Aides" has Butters getting brutally beaten by his parents after Cartman tricks them.
"The Death Camp of Tolerance" has the Tolerance Camp Warden, one of the most cruel and sadistic characters Trey and Matt have ever come up with (besides Cartman), routinely threatens to kill the kids if they don't meet up to his expectations, especially poor Kyle (because the episode in question is based on Schindler's List and Kyle is Jewish.)
The robbers from "Super Fun Time". They even threatened to kill Kenny and were seconds away from pulling the trigger when Stan intervened.
In "Handicar", Timmy's business rivals sneak into his room and break his legs with baseball bats. This would be bad enough if they did this to a normal kid, but Timmy is mentally and physically handicapped. Which is mainly the reason why he's no worse for the wear when we see him soon afterwards - he was crippled to begin with, so he can't move with his legs anyway.
In "Bike Parade", Jeff Bezos callously orders Alexa to kill Kennynote who was shoehorned into protesting Amazon by his father, which she agrees to. The end of the episode reveals that she made good on that claim.
Don Karnage in the pilot of TaleSpin. The worst part; Kit's reaction when Karnage crumbles his board before having his pirates throw the kid off the plane indicates he thought that even Karnage wouldn't go that far...and it happening anyway terrifies him.
Teen Titans had a villain called Cardiac who only targeted children; according to Word of God, this was because he was supposed to be more of an anime-style villain.
In ThunderCats (1985), villains rarely care that Wilykit and Wilykat are children, often taking advantage of that fact to use them as hostages. This becomes especially bad in some episodes like the one with Safari Joe; the Thundrainium he used to restrain the team was hurting them far worse than it was the adults, as Cheetarah pointed out. (Of course, bad guys in the series can be rather cruel bullies, kidnapping, enslaving, and tormenting the peaceful races of Third Earth on a regular basis.)
In ThunderCats (2011), Mumm-Ra and his army consider all surviving cats a threat, including kittens WilyKat and WilyKit. The task force consisting of Slithe, Kaynar, Sauro, and Kask is especially nasty in this regard.
Many villains on El Tigre have no issue whatsoever attempting to maim or even murder main character Manny/El Tigre, with Sartana once preparing to skin him and his father's ex-sidekick wanting him dead because White Pantera chose to marry the woman who would be Manny's mother instead of pursuinghim. Manny's best friend Frida is equally in danger between her relationship with Manny and her dad's status as Miracle City's police chief.
Soundwave and Blackarachnia in Transformers Animated have threatened Sari. The former even tried to make her own father murder her.
There's also Meltdown, who once kidnapped Sari with the intent to do unethical experiments on her.
Megatron from Transformers: Prime. When he found out that he near-fatally poisoned Raf with Dark Energon while shooting at Bumblebee, he was downright pleased.
Megatron: Well, well. It looks as though I swatted a bee, and squashed a bug.
At the end of the Villainous short "The Missing Cases of the Kids Next Door", when the KND is hacking into the Hatbot arm they got, they get a transmission from Dr. Flug, who warns them that if they keep investigating into Black Hat Organization, they won't show any compassion to them, even if they are children. And remember, this is Dr. Flug, who is a wimpy scientist scared to death of his Bad Boss, Black Hat. You can bet his boss is far more evil.
The Joker purposely singles out Robin in battle, which makes sense considering his archenemy.
The Joker: I've always wanted to carve this bird.
Queen Bee has no hesitation in placing the young boy Garfield under her thrall. If she wants, she can easily make him hurt himself. Even creepier, she acts affectionately (in a somewhat twisted manner) toward him while stating her threat.
Count Vertigo was willing to let his own niece, Queen Perdita, who needed a heart transplant, die on the operating table because it would make him the King of Vlatava. Unfortunately for him, Kid Flash reveals the young queen with a recording of the Count's Engineered Public Confession, as he thought he succeeded. It's enough to strip him of his "diplomatic immunity" for treason, and Kid Flash tells the security guards, "Take him to Belle Reve." There the Count is laughed at by the inmates for his failing.