In Pokemon 3: Spell of the Unown, a little girl protects Entei and screams "No More Fighting!". Granted Entei isn't evil - just a bit too much of a Literal Genie.
In the regular PokÚmon series itself, Brock's siblings pull this on Ash to get him to stop attacking Brock's Onix.
Fullmetal Alchemist: Ed and Al discover, to their horror, that five-year-old Nina Tucker's father has performed a transmutation on her and her pet dog to make them into a chimera. Nina's father Shou tells Ed that the two of them are Not So Different, however, as Ed tested the boundaries of alchemy as well by trying to revive his mother. Ed screams "I'm not-like-YOU!!", and starts to beat Nina's father raw in a rage - until the chimera Nina starts to growl and tug at his sleeve; "No, big bwudder." Even Al couldn't stop him before this.
In the manga, Scar of all people gets protected by a girl from Xing named May Chang.
Black☆Star's first mission in Soul Eater ends with him defeating the bodyguard Mifune, only to be 'attacked' by his charge, very young witch Angela, who insists that he leave Mifune alone. Shocked that the witch he was supposedly sent to kill is a little girl, the would-be assassin backs down.
In Gunnm the young girl Koyomi, moved by Den's tirade against Tiphares' callous treatment of the surface dwellers, stands in Alita's way as Alita is prepared to finish Den off. Koyomi declares her intention to join Barjack, and Alita, still remembering Koyomi as the orphan baby she rescued, decides to leave. Den is amused that he was rescued by someone so small and he welcomes Koyomi to Barjack.
In Watchmen, when Rorschach confronts his ex-landlady about her having lied about him. Although none of them directly jump in his way, the presence of her children makes him back down.
In Kill Bill, The Bride and her opponent Vernita Green are interrupted by Vernita's daughter Nikki coming home from school; they both act innocent, and Vernita orders her upstairs. When Vernita makes her attempt to bushwhack the Bride, she puts a knife into her at range — and turns to see Nikki staring at them.
The Bride: It was not my intention to do this in front of you. For that, I'm sorry. But take my word for it; your mother had it coming. When you grow up, if you still feel raw about it, I'll be waiting.
Later on, when the Bride catches up with Bill, she is interrupted in her attempt to, well, kill Bill, by the sudden intervention of their daughter. This doesn't seem to have been planned by Bill, he just happened to be raising and taking care of the kid.
In the original Stargate movie, when presented before Ra, Jack manages to wrestle a weapon from the guards, turns to shoot Ra... but Ra's entourage of children calmly step in front of him, and he can't bring himself to shoot through them.
And then he nukes them, but we're supposed to forget their existence by that point plus Ra had established his credibility as a world enslaving, attempted genocide level villain. In the Novelization, the oldest of them gathers the rest and they jump ship before it blows up.
The Fall toys with this. Although Alexandria is on the hero's side, she still essentially plays this role during the final battle.
The villain of The Bourne Identity is revealed to be saved by this trope for a while, allowing him to cause the injury that led to the titular character's amnesia in the first place.
In The Dead Zone, Smith tries to assassinate a Presidential candidate, but the man uses a child as a shield and he's unable to fire. While Smith gets taken down by security, the candidate's cowardly actions ruin his chances at election.
In Let the Right One In, Oskar is saved from the bullies at the last moment by Eli. Although Eli is, admittedly, not a normal child. That said, he's already saved Eli from almost certain death, so this film has two examples of this trope protecting each other.
Although she was an adult at the time (twenty years old) the trope is otherwise played straight between Elena and Diego in The Mask of Zorro. When Diego is about to kill Rafael, Elena throws herself between them, begging her biological father not to kill the man who raised her.
In Crash, the store owner confronts the repair man who couldn't fix his door after his store is vandalized and threatens to shoot him. The repair man's daughter, watching the confrontation, races out to save her father and throws herself between the two as the man fires. Amazingly, the kid's uninjured and the store owner's shaken by it all, thinking the kid's an angel from Heaven. Turns out his gun was loaded with blanks by his own daughter, who was afraid he'd pull a stunt like this.
Bunch of children in Christmas Evil surround Harry to protect him from their parents who realize that he is the killer Santa responsible for the deaths at the church.
The final book of the Inheritance Cycle does this. When Eragon, Arya, Elva, and Saphira enter Galbatorix's throne room, he is well aware of the fact that they have a weapon that can pierce his wards, and that they have a witch-child who can say the things that need to be said to kill him. How does he solve this? He makes Elva mute until she leaves the room, and he brings in two children, and in possibly the most conversational tone a villain can have, he essentially says "You make one wrong move, and both of them will die. You do anything I don't like and they die. Hell, you so much as scratch your nose when I don't tell you to, and they both die." It works.
A version of this happens in Harry Potter, of all places - subverted in that the aggressor himself is a child, and the defender, a cat. At the end of Prisoner of Azkaban, Harry has Sirius Black defenseless and is holding him at wandpoint, thinking of killing him, when Hermione's ugly, half-kneazle pet jumps over his heart to protect him. Harry ''doesn't rule out killing Crookshanks as well, but he hesitates long enough for someone to come in and stop everything.
Live Action TV
On LOST, when the survivors have Ben captured in season four, Sawyer says that they should just shoot him and be done with it, and Locke responds that he's not so callous that he will kill him while his daughter is right there watching.
Another occurrence of this is when Ben is about to shoot Penny but is stopped when her young son walks out of the boat, and hesitates just long enough to get soundly thrashed by a very irate Desmond, who he had just shot right in the groceries.
An inverted case of protecting the heroine from the Dean Bitterman in Japanese drama Shokojo Seira. Little Romi is the only reason why school Director Mimura Chieko kept Seira in the school or otherwise she would have been kicked out.
Weaponized in Suikoden II, when your army's strategist suspects the enemy leader of setting a trap at a peace summit. He has access to a little girl said leader has a soft spot for, and arranges for her to be present when the trap is sprung. The enemy leader proves unwilling to use lethal force with the girl watching.
Shadow Hearts: Covenant has a rare double-subversion of this trope: Yuri, upon meeting Ishimura, who was planning on adding a new front to the war, and thus more suffering (A rather slimy fellow). As Yuri was about to attack Ishimura, he was confronted by the guy's grandson. Instead of backing down, he pushes the kid aside, and brutally kicked the old man repeatedly, but the subversion gets subverted when he breaks down and is unable to kill him.
In Disgaea: Hour of Darkness, after defeating Hoggmeister, Laharl is about to kill him when the pig's son begs him to stop. If the player's ally-kill count is low, Laharl automatically spares the guy (who joins). But if your kill count is high, you can go to kill him but Flonne will attack you, leading to a nonstandard game over
Nonviolent example in Persona 4; Dojima occasionally presses the protagonist on what he does with his time, with increasing hostility; his daughter Nanako (who also happens to be the Justice Arcana) is an expert on shutting him down.
Celesto: Go home, hug your daughter tight, and thank her for that good-luck pinch. She just saved your life.
Gray was ready to strike Sebastian down, but Mia intervened just in time. One of the reasons Sebastian made it out of there alive.
Done the other way around in "Ayla and the Birthday Brawl" of the Whateley Universe. When Generator and Bladedancer have to dive into a supervillain hostage crisis and one of the Felonious Four is about to kill Generator, one of the hostage children steps forward to save Generator. It only partially works. The supervillain is going to mutilate the kid then kill Generator, but spends so much time threatening them that he runs out of time and has to use the escape portal before he can hurt either.
If I have children and subsequently grandchildren, I will keep my three-year-old granddaughter near me at all times. When the hero enters to kill me, I will ask him to first explain to her why it is necessary to kill her beloved grandpa. When the hero launches into an explanation of morality way over her head, that will be her cue to pull the lever and send him into the pit of crocodiles. After all, small children like crocodiles almost as much as Evil Overlords and it's important to spend quality time with the grandkids.
In Justice League Unlimited, Huntress decided to kill the man responsible for her parent's death before he could go into hiding, the villain was literally at her mercy when the man's son broke free from his escort. She ended up turning her bow away, sparing his life. This is partly because she was reminded of the night when her parents died, so she punched the guy instead.
Near the end of the South Park movie, just before Terrance and Phillip are about to be killed, the kids stand in the way and plead to the army and Kyle's mom not to kill them. This doesn't do much good, as the kids are only about a third T&P's height and though Kyle's speech touches the soldiers, Kyle's mom shoots them dead anyway.
After being a bully for half of an episode of Family Guy, Peter encounters the same bully who picked on him in his school days. He decides to beat him up after what he had done, but before he could do so, Chris beats HIM up and yells at him to stop bullying people.
Some people actually try this in Real Life. Unfortunately, it has a tendency to result in dead children. To everyone reading, remember that while this may generate horrific publicity for the erstwhile child-killer, you shouldn't have done that. Seriously, not cool.
The Westboro Baptist Church bring their kids to their protests, just for this purpose.
Some members of the Occupy Wall Street movement tried this in Washington, using kids to barricade the doors of a convention center and block traffic in the street.
It is speculated that those who designed the Murrah building in Oklahoma City wanted the day care center placed on the second floor, visible to anyone who passed by, in the hopes that seeing the innocent, adorable children playing might deter anyone looking to do harm. As we all know, it didn't.
Baboons, while trying to avoid a fight will hide among infants, as most Baboons won't fight in front of them.
It's a social survival tactic to get in good with mothers and provide babysitting service for them. If you're carrying an infant, you're largely immune to attacks from other males. If a male does disregard an infant and attack the babysitter, the females will swarm him in defense of the infant.
In 2008, there was a news article about a 7-year-old girl and her mother who were attacked by the mom's ex-boyfriend. When he tried to kill the mother, THE GIRL TOOK SEVERAL BULLETS! Amazingly she lived, and the boyfriend will probably get life.
One of Saddam Hussein's tactics was to place his command centres on the top floors of schools to discourage attacks on the commanders.
During the 2013 siege of the Westgate Shopping Mall in Nairobi, Kenya, a four-year-old boy stood between his wounded mother and one of the gunmen, calling him "a very bad man". The terrorist lowered his gun, handed the boy a Mars bar, and said "Forgive me, we are not monsters" before leaving.