In an early scene in Gundam SEED Destiny, the guerrilla fighters in Gibraltar whom Minerva assisted previously are shown executing the Earth Alliance officers they've taken prisoner. This can be interpreted as an early indication that the protagonist may not be fighting on the righteous side, after all...
A much earlier example is arguably Yzak's destruction of a shuttle full of civilians during a battle with Kira. Even if Yzak's assumption that the shuttle contained fleeing soldiers, shooting an unarmed shuttle is still a pretty heinous act.
The entire Fullmetal Alchemist flashback to the Ishval Genocide Campaign is basically one long hideous war crime.
Especially poignant was the death of Winry's parents, who had gone to the battlefields of Ishval for Red Cross-type volunteer duties, and were then killed by Scar during a Freak Out.
Made worse in the 2003-anime where they were killed by a very reluctant Roy Mustang on orders from his superiors, because they healed Ishvalian civilans.
It's worth noting that Armstrong outright refuses to kill civilians. Kimblee kills them instead, but keeps Armstrong from getting in trouble, respecting the strength of his convictions.
In Code Geass, the flashback to Lelouch, Suzaku and the blind Nunnally fleeing through Japan's countryside involves them stumbling onto the scene of genocide in a village. This event scars Lelouch and Suzaku, leading the former to hate Britannia with a vengeance and the latter to be horrified at what had happened, compounded with killing his father, leading him to blame himself for it all. Ironically, Lelouch and Suzaku would both precipitate a repeat of this, with Suzaku joining the Knights Of Round and conquering countries, and Lelouch accidentally causing a country-wide riot, and eventually leading his own massacre, AND ruling the world with a bloody iron fist. (The latter is part of a Thanatos Gambit.)
There's also Tamaki, who's usually just the Plucky Comic Relief of the Black Knights, ordering some of the Ashford Academy students executed after he finds them sneaking around, trying to save Suzaku, who is trapped in the disabled Lancelot. No one actually gets a chance to carry out those orders, though, and the event's never mentioned again.
Worse yet, those civilians were Lelouch's friends... Lelouch, who was Tamaki's superior. Though this is a very unusual situation.
The first episode has Clovis' purge of the Shinjuku ghetto. Cornelia replicates this in Saitama, far more effectively, in order to lure out Zero.
The Emperor Rescue Mission Arc in The Five Star Stories features a scene with the AKD forces (more or less the good guys here) lining up and shooting captured enemy troops as the Morale Officer (actually a member of the Headdliner corps in disguise) begs their commanding officer to call it off.
In the Area 88 manga and OVA, Nguyen kills an enemy pilot who has ejected from his jet.
In the manga, Rocky witnesses anti-government forces slaughter an entire Bedouin camp. When Shin and Mickey fly over the desert carnage afterwards, they're both horrified.
Appears several times in Nth Man: The Ultimate Ninja , often pushing the boundaries of The Comics Code. These include the aftermath of a mass execution of civilians, children hacking to death a wounded soldier in reprisal for said execution, and a bombing run on a field hospital.
Transformers: More than Meets the Eye: Whirl proves that he's a Heroic Comedic Sociopath and a Sociopathic Hero, when he fights Nautilator, and pins him down, Nautilator surrenders and begs for his life, but Whirl is more interested in the fact that the con's voice sounds like Megatron. Whirl tries to make his voice sound like Optimus Prime's to make the confrontation more epic, but gives up, and just executes him.
Transformers: Last Stand of the Wreckers reveals why Impactor is now the former leader of the Wreckers. After defeating and capturing Squadron X, the Decepticon counterparts to the Wreckers, he was told that the world they fought on was in fact neutral territory and that the Wreckers had to release the Squadron or the Autobots would face diplomatic problems. Impactor's solution was to execute all of the restrained prisoners on the spot and convince most of the Wreckers to lie and cover for him, claiming the Squadron had attempted to escape. Only Springer had the conviction to testify against Impactor and reveal the unpleasant truth.
300 tries to play this as entirely justified and even admirable, which its iconic scene of the heroic and manly king of Sparta kicking an unarmed messenger down the well from Army of Darkness.
In Shell Shock, this trope is chillingly partnered with Sadistic Choice. A truckload of captured zebras are machinegunned in the middle of the road.
In Boys Do Tankary, during a flashback, some of Vincent's men rape and murder some teenage POWs. Only Vincent's intervention saves the youngest, Nyra, and as a result, he and Nyra are locked in a room, given a month to kill each other. Vincent is ultimately forced to kill Nyra at her request, or so he thought at the time.
Films — Live-Action
Flags of Our Fathers and Letters from Iwo Jima both showed the protagonists of both films (American in the former, Japanese in the latter) killing enemy soldiers trying to surrender by stabbing them with bayonets (and setting them on fire in one case). Known to have actually happened quite a bit in the Pacific Theater on both sides, as it was common for a surrender to be a ruse instead.
The shooting of surrendering Czech conscripts by American troops during D-Day.
The mental torture of the German soldier after the assault on the machinegun nest, with Reiben threatening to desert The Squad if they don't execute the German and Horvath threatening to shoot Reiben if he doesn't obey orders and get back in line. When Upham kills the same German trooper that was captured but set free earlier, while he's surrendering, but only after Upham saw him deliberately shoot Captain Miller, the man who let him live.
A German soldier is seen abusing captured Russian prisoners of war.
A temporary cease-fire to gather the wounded from the battlefield is broken by a suspicious German soldier.
The unsympathetic German officer orders the soldiers to shoot some Russian civilians who have been taken prisoner, saying they were found trying to commit sabotage. The protagonists state to themselves that the sabotage allegation is nothing more than a pretense to shoot the prisoners because they're running out of food to feed them, and one of them is a child who they themselves took prisoner and befriended. They hesitate before finally being intimidated into doing it.
After discovering a German officer's stronghold, the German soldiers find Russian sniper Irina who has been tied to a bed and raped. The protagonists even suggest taking turns to 'use' her before Leutnant Von Witzland puts a stop to it.
In The Longest Day, there is one brief scene with an American shooting a German soldier who is unarmed and trying to surrender, saying, "Bitte, bitte!" The American soldier says, "I wonder what 'bitter bitter' means." It was later found that, historically, the medic that shot the Germans spoke German, but had a "take no prisoners" policy.
Apocalypse Now: Willard shoots the badly wounded only survivor of the accidental attack on the sampan, to avoid having to take her for medical attention and to make an example of the crew.
Arguable non-war movie example: The extended version of The Two Towers movie shows Faramir's troops brutalizing Gollum in hope of getting him to talk. This scene was cut for the theatrical version.
In The Hurt Locker, an American Army officer opts to withhold medical treatment from a wounded insurgent who would otherwise survive. It's implied the insurgent is shot shortly thereafter to hasten the process.
Sergeant Meserve in Casualties of War kidnaps, rapes, and kills an innocent Vietnamese civilian, which is the main plot of the entire story, and the other soldiers' reactions.
An American door gunner is randomly shooting civilians as they fly over rice paddies.
Gunner: Anyone who runs is a VC, anyone who stands still is a well-disciplined VC! You guys oughta do a story about me sometime! Joker: Why should we do a story about you? Gunner: 'Cuz I'm so fuckin' good! I done got me 157 dead gooks killed. Plus 50 water buffalo, too! Them's all confirmed! Joker: Any women or children? Gunner: Sometimes! Joker: How can you shoot women or children? Gunner: Easy! Ya just don't lead 'em so much! (laughs) Ain't war hell?
Joker covers the story of a mass-grave where 20 civilians executed by the North Vietnamese Army lie, some of the victims were buried alive.
Pretty much everything Bunny does in Platoon, including beating a crippled Vietnamese civilian and his elderly mother to death just for the hell of it, and nearly raping a young girl.
You have to really look for it, but in Pan's Labyrinth, after the rebels win their battle against the fascists, they proceed to shoot their captives to death.
Battle: Los Angeles has a particularly disturbing scene where the Marines have grabbed one of the wounded alien invaders. The Marines had previously emptied entire magazines into individual invaders to little effect, so Staff Sergeant Nantz has his men hold the alien down while he and a local veterinarian rip, cut, and stab at the still-living alien's body in search of a vital point. Once they find a point to aim for, the Marines become a lot more effective at bringing down the invaders. Unusually, the movie doesn't present the scene in either a negative or positive light; the viewer is left to determine whether or not the act is justified or heinous. The aliens themselves have a take-no-prisoners policy, and dead civilians can be seen throughout, as it's stated the aliens shoot up everything living in sight.
The Dirty Dozen has been criticized for depicting war crimes: in one scene, Lee Marvin's character orders that a group of surrendered German soldiers be summarily executed. A later scene in which a group of German officers and their wives/mistresses are killed in a basement has also been cited as an example, though in the context of the mission the killing of the women would more likely be classified as collateral damage.
The whole point of The Whistleblower. The UN peacekeepers stationed in 1990s Bosnia are importing girls to be their sex slaves. Based on a true story.
Play Dirty ends with the only two survivors of the squad (With the possible exception of a man left behind with a mortal gut wound who potentially hadn't died yet) being gunned down by a British soldier who saw their white flag (they were disguised as German soldiers) and shot them anyway. The killer's CO simply said "Don't do it again".
The sailors in Das Boot return to sink an already-torpedoed ship and are shocked to discover there are still people on it, because the rescue ships failed to arrive. However, since they can't take prisoners either, they have to leave them to drown.
Animorphs: In "The Hork-Bajir Chronicles", we discover that the (up until now apparently innocent) Andalite host of the leader of the Earth invasion killed thousands, if not millions, of Hork-Bajir in an effort to keep that planet from falling into enemy hands. By creating and releasing a virus that will break down the DNA proteins unique to the Hork-Bajir, meaning a peaceful race whose resistance movement has been of tremendous help has over half their population die by having their bodies disintegrate slowly and painfully.
A recurring theme is to what degree the Animorphs' actions are war crimes, especially since the Puppeteer Parasites they fight a.) are helpless in their natural form and b.) cannot be harmed without hurting their host if they are given a fighting chance.
Probably the best example of this trope is the second to last book, where Jake has a pool of 17,000 Yeerks dumped into space for no good reason.
A Song of Ice and Fire has all five sides in the war committing terrible war crimes. The worst were committed by Tywin Lannister's outrider troops, although Robb Stark's army were incredibly brutal to the peasants in the allied Riverlands (though to be fair, the commander of this army was Roose Bolton, who neither asked nor cared for Robb's approval, and simply did it. Plus he later sold Robb out to the Lannisters). Tavern wenches who slept with Lannister soldiers were likewise executed and hanged from trees, their bodies left to the crows.
The Sword of Truth series has shades of this, where there are several drastic and questionable actions the hero takes (having a prisoner tortured, mowing down peace protesters, imposing total war). Sometimes averted, where it's treated as if the hero doing this is completely right and just (the peace protesters), while in other places it's justified as the only option he has left (the total war).
It's always portrayed as totally right and just, the only distinguishing factor is how long they spend providing self-justifications. At one point Kahlan explained how torturing a captured soldier to death as slowly as possible was the right thing to do so he (who saw himself as a martyr) could understand how important life was.
It comes up in Discworld novels from time to time. Fred Colon mentions beating prisoners of war mostly because you just saw an arrow go through your friend's face and you're looking for the first son of a bitch in the wrong uniform to make an example of. In Monstrous Regiment, Sergeant Jackrum intentionally arranges things so that he can murder a POW, although in this case it's because he doesn't have the luxury of keeping him as a prisoner.
No Hammer's Slammers novel would be complete without at least one graphic description of what happens to civilians who get caught in the crossfire.
In the climax of Run Silent Run Deep, the hero has his submarine Sink the Lifeboats to make sure a particularly effective Japanese destroyer captain will never sink another American sub. His crew obey orders, but they're shocked.
In the sequel Dust on the Sea it is made obvious that the American captain's own mileage varied.
In the last book of Harry Potter, Harry himself uses the "unforgivable" torture-inflicting Cruciatus curse to ambush a Death Eater—and reminds us that for the curse to work, you have to genuinely want the target to suffer.
In The Five People You Meet in Heaven, a war crime is the main impetus for the plot. The protagonist is Eddie, a World War II veteran who fought in the Pacific. He ends up being held as a prisoner of war, but he and the others manage to escape. After escaping, they burn the camp down. Eddie ends up thinking that there is a little girl inside one of the huts near the camp and tries to run back into the hut, but is shot in the leg. After he dies (years later at the age of 83) and goes to heaven, he meets, among others, the little girl that was in the hut.
In the final book of the Timeline-191 series, Sociopathic Soldier Boris Lavochkin orders several massacres of civilians, including the murder of an entire village. So as well as an expy of Nazi Germany in form of the CSA, Turtledove also provides an expy of war crimes committed by the Red Army.
Ronald Speirs' execution of German POWs. Historically, Speirs had a reputation for killing German POWs, but it was never confirmed if he indeed had. Stories were passed through the company and battalion, but rumors were, according to the soldiers interviews, probably embellished, and Speirs was known to believe that having his own troops fear him wasn't necessarily a bad thing. The truth of what he did or did not do died with him.
He is shown to politely offer the Germans smokes and then the camera moves to another soldier who watches in horror as bursts from an SMG are heard. Speirs later gets amusement out it by offering some GIs a cigarette in another episode, just before he's given command of E Company. Speirs' deadpan expression while the scared-shitless men take the offered cigarettes is a Crowning Moment of Funny.
The "did he or didn't he" aspect of Speirs' reputation was explicitly pointed out during a conversation with Lipton.
Speirs: You want to ask me, don't you?
Lipton: Ask you what, sir?
Speirs: You want to know if they're true or not... the stories about me. Did you ever notice with stories like that, everyone says they heard it from someone who was there. But then when you ask that person, they say they heard it from someone who was there. It's nothing new, really. I bet if you went back two thousand years, you'd hear a couple of centurions standing around, yakking about how Tertius lopped off the heads of some Carthaginian prisoners.
Lipton: Well, maybe they kept talking about it because they never heard Tertius deny it.
Speirs: Well, maybe that's because Tertius knew there was some value to the men thinking he was the meanest, toughest son of a bitch in the whole Roman Legion.
In the 9th episode, E Company passes by while some French soldiers execute German soldiers they found hiding with little more than a shrug. This serves as a quick introduction to War Is Hell for an eager New Meat named O'Keefe.
Half of Easy Company break the rules of war at some point. All the loot they carry around is actually war crime material.
The Pacific has one poignant scene where US Marines are torturing a Japanese survivor of a banzai attack by shooting him in the arms and legs. The last Japanese soldier they tried to take prisoner blew himself up along with a couple of Marines, so they are not taking prisoners.
In one scene, a Marine is cutting the teeth out of a live Japanese soldier's head while the soldier screams in pain. Snafu shoots the guy in the head, putting him out of his misery, while saying that it "makes it easier". Although it was legal to take war trophies, taking the personal effects of dead soldiers was not allowed. This included the mutilation of bodies and the removal of their gold teeth.
In another scene, after a last-ditch suicide charge by the Japanese, Sledge shoots a soldier who was unarmed and wounded. Later in the same episode, he decides not to shoot another unarmed Japanese soldier - but then a few rookie marines gun him down instead and blow off Sledge when he disapproves.
Marine: We're here ta' kill Japs ain't we?!
In one scene, a wounded soldier who is no longer a threat is seen being choked to death.
Occurs much higher up in the ranks than most examples of this trope, but in the The West Wing episode "Posse Comitatus", President Bartlet is forced to assassinate a terrorist-sponsoring foreign defense minister and lie about it to avoid having to embroil the Middle East in a war. Doubles as one of the heaviest examples of The Chains of Commanding in the show, and one of the biggest Tear Jerkers.
In Falling Skies, when the aliens order a mech to mow down a group of kids, as an example of what happens when the humans attempt to free one.
Also done by the humans, when the doctor is about to try and vivisect a prisoner, but is stopped.
On Alphas an attempt by government agents to arrest the leaders of Red Flag (an Alpha terrorist organization) gathered for a meeting quickly descends into chaos as some of the Alphas resist and the government agents open fire. They kill everyone they see, even those trying to surrender or hide. They shoot Bill (in his vest), failing to distinguish him from their targets after a demonstration of Super Strength. One agent nearly kills Gary when he has a tantrum over finding Anna's body - given that he weighs ninety pounds soaking wet and can barely lift the baton he was whaling on the agent with, it comes off very much like a Nazi about to stomp on a yapping chihuahua. The scene demonstrated how unprepared and heavy handed the government is when dealing with Alphas and that the situation has reached the level of a war.
Two such instances in the 1997 miniseries The Rough Riders. One involves a Spanish soldier who tries to surrender, but after he's already killed one of the Rough Riders. He's promptly shot. The other is the rather casual bayoneting of a German military adviser. The German's death is fictional, as no such incident is known to have occurred and indeed the presence of German military at the battle is disputed by historians. Why director John Milius would invent a fictional war crime unnecessary to the plot is not known, however he refers to the Germans bizarrely and inaccurately as Nazis on the DVD's audio commentary, suggesting a mild axe to grind even against pre-World War II Germans.
JAG: The promotion of Rear Admiral Thomas Boone to Vice Admiral is called off in "A Separate Peace" because of credible sources claiming he took part in war crimes during The Vietnam War when working closely with CIA officers.
In True Blood, Terry Belflaur and all the other Marines are war criminals, committing some seemingly harmless acts, such as holing up in a mosque, but also for more harmful crimes, such as killing harmless and unarmed civilians.
In German war drama Unsere Mütter, unsere Väter, the Winter brothers' unit is seen shooting Russian POWs, pushing civilians at gunpoint onto a mined area to clear their path, and carrying out reprisal killings against innocent farmers for the actions of partisans (not that the Russians are much better, during the little we see of them). And the crimes Friedhelm commits at the behest of SS-Sturmbahnführer Hiemer are even worse.
In William Shakespeare's Henry V, the hero-king threatens the citizens of Harfleur with some pretty grisly consequences for trying to defend themselves ("In a moment look to see the blind and bloody soldier with foul hand defile the locks of your shrill-shrieking daughters", etc.). He goes on, at Agincourt, to order his soldiers to slaughter all their prisoners (the text of the play actually has him doing thistwice, which is a little weird). In the next scene this is explained by Captain Gower as retribution for the killing of the boys looking after the baggage (and many readers of the play are inclined to take his word for it), but the first of these orders is given before anyone on the English side learns of it, in response to the French regrouping.
The Harfleur sequence is a case of Values Dissonance. In medieval warfare it was the norm that a besieged town would surrender after the walls were breached. If the garrison did not surrender but continued to fight, that would be a sign of 'no quarter' and followed up by the attackers with a total sack of the town.
The prisoners were presumably against it, but it must also have been a very unpopular order among his own army. Many of them had captured French knights that would otherwise have paid hefty ransoms. (Henry's kill-em-all order is the reason that his old drinking buddy Pistol looks forward to a future as a pimp and thief: he could have retired comfortably on the ransom his prisoner M. Fer would have brought him.)
In Real Life, the English archers did the slaughtering of prisoners. Being merely commoners, they would not have expected good treatment if they were captured, and they'd have seen none of the ransom money if the French were ransomed back after capture. Also, the order for the slaughter wasn't a form of Disproportionate Retribution, but rather to prevent the French knights from rearming themselves and attacking the English behind their palings. Even the French sources at the time don't call him out on it.
Call of Duty 4 shows how neither side is saintly, and both the U.S. Marine Corps and the SAS will use brutal techniques to find out what is going on.
Call of Duty:World at War goes even further. The Pacific campaign starts with your character being tortured by his Japanese captors, and features ambushes from units playing dead, booby traps, and kamikaze attacks. In response, the Americans employ flamethrowers to great effect. The Eastern front has the repeated execution of wounded soldiers, the razing of crops and homes, and the massacre of surrendering soldiers... and that's as the Russians.
Modern Warfare 2 ups the ante even further with the infamous 'No Russian' level, where the player, as a deep cover CIA operative tasked with getting in the good graces of the villain of the game, participates in a terrorist attack on a Moscow airport, complete with the gunning down of unarmed civilians. In retribution for that mission, the Russians invade Washington, D.C. with the sole intent of killing as many Americans as possible. The player gets a front-row view of Russian tanks and helicopters firing on CASEVAC choppers (i.e., civilian evacuation helicopters). In the rules of war, that's what we call a definite no-no.
In the middle of the "Project Nova" level of Black Ops, Kravchenko is seen executing surviving German prisoners with his pistol as they beg for mercy. As he reaches the last one, he runs out of ammo, and uses his knife to kill him. Later that mission, Kravchenko and Dragovich betray half of the Soviet squad by gassing them to death in order to test out Nova Six.
In the beginning of "Payback", Bowman has his skull crushed by a pipe wielded by the Russian interrogator. Woods and Mason then are forced to play Russian Roulette with each other.
In the mission "The Defector" the entire civilian staff of the MACV compound is executed by the NVA for collaborating with American forces. Supplemental intel found in the level indicates that off-screen, hundreds of other civilians are similarly massacred for alleged "collaboration" after the NVA capture the city.
Fictitious war, but Fallout 3's Operation Anchorage features an American soldier executing 4 Chinese prisoners. Killing the American before the shooting causes your allies to turn against you, and try to kill you and the prisoners. Turns into Refuge in Audacity when injured American soldiers come out of the hospital, in underwear, in an Alaskan winter, and attack you with grenades. However, to balance things out, when you storm General Jingwei's camp, you see him executing American prisoners with his lightning sword.
In one Terran mission of Starcraft: Brood War, a civilian technician runs into a squad of UED marines who kill one of his colleagues to convince him to cooperate. When he does, they thank him... then shoot him anyway. One of them even quips "Err... oops. Heh heh heh..."
In the first mission StarCraft II, the Terran Dominion are rounding up civilians for labor in a mining site, one of them tries to run, and a marine shoots him.
In Mass Effect, if you pick the "Ruthless" reputation, you sent many of your men to certain death in order to defeat a batarian position - and then massacred the surrendering batarians.
Games with moral choice systems frequently give you the option of doing this yourself.
Happens from time to time in World of Warcraft, such as early on in the Jade Forest, when Admiral Rogers orders her troops to open fire on Horde soldiers swimming away from their sinking ships and trying to surrender. On the other hand, some of the atrocities that the Forsaken and Garrosh commit are viewed with disgust by much of the rest of the Horde (in the former case, even Garrosh).
Several events were added to the game to drive home the fact that Garrosh has gone beyond the pale. During the Darkspear Rebellion the player sees trolls being caged, executed, and burned in piles while orcs laugh. Early in the Siege of Orgrimmar a cinematic shows the destruction of Vale, a holy place to the Pandaren, due to Garrosh's actions.
Literally the very first discussion you hear on the Soviet side in Command & Conquer: Red Alert is about the testing of nerve gas — on both adults and children. This is followed by your actual mission: "Go at once to Torun, destroy everything and everyone. No prisoners, no survivors."