Batman Returns: The Penguin crosses the Moral Event Horizon when he tries to have every firstborn son of Gotham City, including very young children and babies, kidnapped and drowned in the sewer as revenge for his parents having tried to do the same to him long ago for being different.
Henchman: Penguin... I mean, killing sleeping children. Isn't it that a little, uh...
Penguin:(kills him) No! It's a lot "uh"!
Cape Fear: Max Cady spends the entire movie plotting to rape a little girl, and he almost succeeds at the end.
Children of the Corn (1984): Said children have been brainwashed into thinking anyone over 19 should be killed. Burt and Vicky mostly attack the older children but the ending has a hilarious moment where they knock out a girl no older than eight (she was coming at them with a scythe).
Burt: Should we do something for her?
Vicky: Let's send her a get-well card from Seattle.
The Devil's Backbone: Jacinto threatens and harms the children of the orphanage. He threatens Carlos by cutting his cheek with a knife, and that's the least of his offenses. He drowned an injured boy because he feared he will be blamed, and ultimately blows up the orphanage, killing some and injuring many children just to get to open a safe.
Dirty Harry: The Scorpio Killer, a psychopathic criminal whose mere existence seems to be to rob, kill, extort ... whatever, and humiliate San Francisco Police Inspector Harry Callahan in the process, has no qualms about using violence against children. In one scene, he shoots a young African American boy (offscreen); in another, he kidnaps a young teen-aged girl, rapes her, and buries her alive (before daring Callahan to find the girl, all for his own amusement). Later, he holds hostage a school bus full of children and ... when several of them refuse to sing "Row, Row, Row Your Boat" he slaps them hard (including at least one girl and two boys). In the climatic scene, Scorpio holds a young boy hostage and threatens to kill him if Harry refuses to surrender; however, Callahan sees an opening and shoots Scorpio, badly wounding but not (instantly) killing him.
After Mina rises from her grave as a vampire in Dracula (1979), her first order of business is to feast on the blood of a baby of one Dr. Seward's patients. To drive in further the horror of the deed, poor boy's bloodless corpse is shown in a closeup.
The setting of Evil Laugh used to be an orphanage until its caretaker Martin killed all the children when he was accused of molesting them.
The whole film Evilenko revolves around a serial killer who targets children.
Eyewitness (or Sudden Terror in the US): The film is about a young boy (Mark "Oliver Twist" Lester) who witnesses an assassination, and the assassins will kill anyone in their path to get him - including our hero's friend Ann-Marie, a little girl around his age.
Final Destination: There's a baby onboard the plane that Death blows up in the first movie. He also crushed a young teenage kid under a plate glass window.
Freddy Got Fingered: Played for "laughs" in a scene where Gordon (Tom Green in the key "protagonist"(?) role) takes the umbilical cord of a newborn baby and - while still attached to the infant - twirls him around like a toy, as though it would do no harm.
Full Metal Jacket: The machine gunner in the helicopter is asked by Joker how he can shoot women and children. He misinterprets the question (probably deliberately).
Gunner: Easy! Ya just don't lead 'em so much!
Ghost Ship. The two murderous crewmen and by extension, Ferriman, during the mass murder montage on the Graza have no qualms towards killing Katie, a scared young girl.
The Hard Way: The Party Crasher, whose previous victims include a four-year old.
Hellraiser: Bloodline: Pinhead decides to torture John Merchant's son to compel him to undo his designs that could destroy the Cenobites.
Heroic Trio: The Big Bad is kidnapping babies in order to raise an evil army. At one point, he pretty randomly kills a baby.
Home Alone (the first movie): Harry and Marv repeatedly threaten to kill Kevin, and would have managed it at the end if Marley hadn't stopped them. In the second Home Alone movie, Harry has a gun at Kevin's head and is about to do him in once and for all (right before the pigeon lady distracts the crooks by dousing them with birdseed and letting the pigeons do the rest).
Harry: I never made it to the sixth grade, kid. And it doesn't look like you're gonna, either.
Jonah Hex: Several of the villains. Quentin Turnbull deliberately waits until some unsuspecting families come up to his bombs before detonating them.
Looper: Much of the plot revolves around Old Joe finding and killing kids he thinks might grow up to become the future leader of the criminal organization he used to work for, and Young Joe trying to protect one of those kids.
Malice: It's revealed that Tracy got pregnant for the sole purpose of miscarrying and therefore looking even more sympathetic to the jury in her medical malpractice case—she's suing her surgeon for removing a healthy ovary, thus causing her not only to miscarry but robbing her of her chance to ever have children of her own. The viewers soon learn that she and the doctor are in on the scam together, and when her estranged husband threatens to reveal their scheme, she plans to kill the child who he claims has witnessed her and the doctor's nefarious activities
Moonwalker: The bad guy, Mr. Big, is pushing around and slapping a girl right in front of Michael Jackson simply to piss him off.
The Mummy Returns: Ankh-Su-Namon threatens to put poisonous snakes in his bed and Lock-Nah actually does stab his hand and only misses because Alex is wearing the bracelet of Anubis. He always manages to escape serious damage, but there's still plenty of evidence that evil does not have standards here.
The Night of the Hunter: ReverendPowell threatens his stepchildren with torture in order to find out where they hid the money their dad had stolen in a bank robbery. He would have done it, too, if they hadn't escaped. The worst part? He wasn't just going to torture them. He was going to torture them in front of each other so that one of them would spill the beans in order to get him to stop torturing the other.
The Final Conflict (the third movie in The Omen film series): A now-grown Damien (Sam Neill) gets his followers to kill all babies born on a certain date, in order to stave off the Messiah. These followers include Scouts ("We're here to do our good deed for the day") and a priest who drowns a baby (offscreen) during a baptism.
¿Quién puede matar a un niño? (Translation: "Who can kill a child?"): The entire premise of this 1976's infamous Spanish horror film. A subversion, in a way, since the KidsAreEvil, of course - and how.
The Raid: One of the SWAT troopers shoots a young lookout in an attempt to stop him blowing their cover. Unfortunately, it fails.
Richie Rich: The villains are more than willing to shoot children, turn them into bedpans and blast them with lasers.
Ronin: Gregor will kill anyone, and his onscreen victims range from a teenage girl to an old man. At one point he tries to shoot a young girl to prove the point.
Sleepy Hollow (Tim Burton's): The Headless Horseman is sent to murder the midwife of the town and her family. He gets the dad right away and the midwife hides her young son under the floor to protect him. She's killed next. The Horseman seems about ready to walk away...before stabbing his sword into the floor. The next scene shows him dropping something into his sack as he leaves the house.
Another scene involves an autopsy of one of the female victims. When examining her abdomen, they notice a strange stab wound. It turns out the Horseman also beheaded her fetus.
Averted in a flashback scene where the Headless Horseman merely shushes the Archer girls rather than kill them.
Spider-Man: The Green Goblin breaks the cable on a lift car housing a group of school children in order to present Spiderman with a Sadistic Choice. He lefts go of the cable, leaving the car to fall and crash. When Spiderman grabs the cable, the Goblin attempts to beat him until he drops it.
Plus Sweeney himself; though he doesn't actually end up killing Toby he demonstrates his willingness to do so on two separate occasions.
In Ted, John nonchalantly sucker-punches Robert, a Creepy Child charging at him. His girlfriend is horrified, to which he responds that someone had to Joan Crawford that kid.
Terminator 2: Judgment Day: The T-1000 is perfectly willing to murder a ten-year-old boy if it means killing the future leader of the human resistance before he can grow up.
The Third Man: The dead Harry Lime faced allegations of racketeering in diluted penicillin, which was lethal. Said penicillin made its way to children's hospitals to treat meningitis, and he allegedly continued the trade knowing where the fatal drugs were going. All these allegations are true.
The Untold Tale: The main character kills a family due to a money dispute. It would be one thing if the family only had one child but the filmmakers saw fit to give the husband and wife as many kids as possible.
The Untouchables: In the opening scene, gangster Frank Nitti leaves a bagful of bombs in a soda bar, right next to a little girl who's talking to the barkeep. Although the bombing was a for-profit crime, there's no obvious reason why he couldn't have waited until the girl left the premises before blowing the place up.
Warlock: The title character skins a young boy because he was an unbaptized firstborn son, which means he can use the boy's fatty tissue for a spell that will allow him to fly unguided. He also takes note of a priest's pregnant wife, and threatens to kill the man's unborn children if he doesn't cooperate.
Watchmen movie: There's the child abductor the Rorschach kills, as in the comic version listed above, and also the Comedian, who gives us this line:
Comedian:"I've done some bad things.. I've done bad things to women..(sob) I even shot kids! But that was fucking war..."
In White House Down, one of the terrorists slaps the 11 year old daughter of the protagonist because she recorded the terrorists faces and uploaded it online in an attempt to help the government figure out what was going on. Throughout the film, she is threatened with guns and roughly dragged around by very strong men. Later, towards the end, the leader of the terrorists threatens to shoot her in the stomach if her father doesn't give up the president and kill her if the president doesn't give up his nuclear launch codes.
In X2: X-Men United, when Lyman asks Stryker why he's keeping the mutant children alive, his response is chilling.
Stryker: I'm a scientist, Sgt. Lyman. When I build a machine, I want to make sure it's working.
In X-Men: The Last Stand, Magneto's assault on Alcatraz involved killing Leech. When Juggernaut is ordered to do it, he replies "With pleasure."
Bolivar Trask and the people working on the Sentinel program in X-Men: Days of Future Past. It's subtly confirmed when Mystique finds the autopsy reports, one of which belongs to Sean Cassidy (Banshee). It's very likely that Sean was still a teenager when he disappeared.