MOTHER 3 plays with it. In Chapter 2 when Oshe Castle is crawling with Pigmasks they attack you and you bring them down like normal enemies. Come Chapter 3 you're playing as a member of their army, and now you're free to talk to the same Pigmasks in the castle who all have dialogue revealing they're all normal people. From then on you get more than a few reminders that they're people by getting hints to their personal lives, their taste in music, and even one that was a kid from your hometown. It doesn't stop you from bringing them down without abandon, though.
Subverted frequently in No One Lives Forever. The player can listen to conversations between mooks which are often fairly long and go into a wide variety of subjects, including, quite often, their personal lives. The player almost always has no choice but to kill them during or after the conversation. How are those German guys going to start a band now?
In Uncharted 2: Among Thieves, Drake has the Lazarevic at his mercy finally, and he tries to tell Drake that "We're Not So Different, you and I". This immediately makes him unable to pull the trigger on him, despite having no problems killing hundreds of human enemies throughout the game. Or, he saw an opportunity for the guy to experience some poetic justice and be torn apart by the Guardians. Besides, Drake was using an M4, which is just a pea-shooter on someone who drank from the Tree of Life.
There's another, slightly strange instance of this early in Uncharted 2; in the early museum break-in level, there's a scene where Harry offers Nate a pair of pistols. Nate is horrified by the prospect of shooting at the innocent guards until Harry reassures him that they're just non-lethal tranquillizers. Shortly after this scene though, there's an in-game sequence where Nate, hanging from a ledge, tosses an unsuspecting guard off the roof and hundreds of feet down the cliff below. Harry makes a quip about the guard's demise, and the two proceed as though nothing had happened.
If you look closely enough you will see that the guard lands in water and swims away.
Penny Arcade also dealt with the seemingly suicidal Uncharted henchmen in Working Conditions.
Commented on in Ghost Trick. One of Sissel's powers is saving the lives of others by changing their fates. However, he defeats hitmen Jeego and Tengo by dropping heavy objects on them, crushing them apparently to death (we even see Jeego's body comedically flattened against a rolling wrecking ball). Sissel muses whether, if he killed Tengo, he'd then have to go back and save his life. He doesn't. In fact they're not mentioned again, even in the epilogue.
Partially averted in the ending of the first Metal Slug, where a paper airplane is shown flying over past stages full of the bodies of mooks you slaughtered. Towards the end, you see a grave with a crying woman standing before it.
Or, if you finish the game with two players, you could see them relaxing and having a time doing stuff other than being, you know, evil.
This trope is mentioned at one point in Xenogears by a random NPC in Kislev, which is for a portion of the game portrayed as the Evil Empire to Aveh's Kingdom:
Unnamed Kislev soldier: Even nameless soldiers have lives to live. Remember that...
Played with in Tales of the Abyss. Most of the party has no qualms with cutting down a dozen mooks who get in their way (even the 13 year old girl), but The Hero Luke goes into a brief Heroic B.S.O.D. after he first kills an enemy soldier. Afterwards, it's mentioned that whenever he kills someone, visions of their death haunts his dreams, and he has a unique victory dialogue against human enemies.
Fire Emblem: Thracia 776 averts this by giving the option to spare Mooks and bosses. Though the game is already Nintendo Hard enough and doing this only makes it more difficult (except it allows you to steal their stuff- so it's give or take, because the path to many of the Game Breaker items is by sparing them).
Fire Emblem touches on it in a few other areas, for example one chapter in the 9th game has you fighting rebels fighting against an underground slave ring, in this chapter you are awarded for killing as few as possible, in another, a villager mentioned you killed her son in the last battle. In the 10th game, the perspective is flipped to that of the enemy side from the 9th game, and it is portrayed in a significantly different light.
Fire Emblem: Shadow Dragon has a chapter that ends with Marth enlightened by a villager that most people working for enemy nations are not completely rotten and some instead would prefer to fight for his cause, if not for their nations' tight grip on them. The conversation ends with Princess Nyna imparting words of wisdom to Marth: "Not all evils are wrought of evil purposes. Perhaps this sounds naïve, but... A true leader needs to look at his opponent and see more than just an enemy."
Fire Emblem Awakening discusses this in Henry and Ricken's B support. After Henry tells Ricken about some of his fellow Plegian soldiers Ricken becomes depressed, realizing he can't see the enemy as faceless blobs with axes anymore. Henry, on the other hand, doesn't mind. He even thinks Ricken's weird for caring so much.
In The Mark Of Kri, murdered bandits will crawl, squrim, or even cry on the ground for a little while after being killed, unless Chunky Salsa'd. It's not fun to watch.
In the final mission of Syphon Filter 2, Gabe Logan and Jason Chance have a Circling Monologue in which Chance calls Logan out on killing hundreds of agents over the course of the game who were just trying to do their job.
Though in balance to this, the Syphon Filter series had several missions where you were forced to avoid killing certain enemies, even assisting them in battles despite the fact that if they saw you, they would shoot you on sight. Syphon Filter 2 especially loved doing this with escaping the airfield guarded by military police, the Moscow club and streets with Russian police, and avoiding as well as assisting the NYPD in the streets of New York.
And in one particular example, there was Teresa's flashback mission in Syphon Filter 3 of her time in the ATF dealing with a Survivalist compound, where at first you work for the ATF, but soon switch over to the Survivalists when you realise the ATF's more devious intentions of a Waco-style cover up.
Perfect Dark, being a FPS, has tons of mooks to mow down. No moral problems on shooting the folks intending to ventilate the President or your personal friends. But many levels take place in regular old buildings, where it is fairly obvious that the guards were just hired hands. You CAN knock them out and disarm them with your fists, but with the exception of a single named villain (who has a key card you need that stops working if she dies) and one objective that requires you KO someone (so they can be interrogated), not expected or required.
GoldenEye (1997). It's perfectly fine to shoot soldiers, who have no say in what they're doing and are really just being paid to defend whatever complex. Even the ones who are just standing in a bathroom stall taking a whiz. But kill a scientist, who is actively involved in creating weapons of mass destruction, and you fail the mission. To be fair, the missions where scientists are in military installations (like Facility and Missile Silo), where the scientists could be compelled to work, and the fact that the West has interests in getting them to defect rather than killing them, which also justifies this.
If the film or reality are any indication, the troops posted to the complex, and the scientists directing the work, almost certainly consider it an enviable posting in terms of salary, benefits, etc. Otherwise, the complex wouldn't remain a secret for long, and what would keep them from sabotaging the machinery and getting everyone killed? As with Bond himself, they may simply be following orders.
Having them defect or captured off-screen, however, would be justifiable.
In the original Fallout, the mooks consist of raiders who Kick the Dog for laughs, ghouls who have all the sentience of a rabid cheetah, and ordinary men and women who were forcibly mutated and brainwashed by the Master. And you kill all three indiscriminately. Appropriately enough, after you kill one Super Mutant, you can find his girlfriend in another room, sobbing inconsolably and cursing your name (in Fallout 2, many of the surviving Super Mutants have settled down following the Master's death and aren't quite so hostile).
This being Fallout, you can kill everyone you see or never kill anyone (unless the plot calls for it).
And in Fallout, you can avoid killing anyone, even setting off an Evac alarm when you blow up an enemy base.
Plus, the Super Mutant-ization process typically reduces them to a beast-like state, and many or all of them have been brainwashed by The Children prior to being dipped.
Fallout 3 has plenty of raiders, soldiers, and guards that constantly respawn for you to kill and are indistinguishable from one another. In the case of raiders, the majority are torturers, murderers, and rapists, so it's hard to feel any regret for decapitating them with a chainsaw and placing their head on a pedestal for all to see. This still does occur near the end of the main campaign, when the player faces off against The Dragon and has the option of sparing him. Sparing him is treated as a moral and noble action by others you speak to, despite the fact that you've slaughtered several dozen of his soldiers to get to that point. To be fair, said Dragon was painted in-game to be a Well-Intentioned Extremist with some Kick the Dog moments to compensate, and a comparatively sane goal. The main reason you are fighting him is because he happens to be loyal to The Enclave.
On the other hand, have this option taken, you can spare two Mooks along with The Dragon. Otherwise, they are doomed.
At the end of Broken Steel, you invade the Enclave's main base, killing a number of scientists along with their soldiers. Tragically, it is revealed in Fallout New Vegas that one of those people was ED-E's creator.
Fallout: New Vegas plays this trope straight at the conclusion of its Honest Hearts expansion. If you choose to destroy the White Legs, you'll find Joshua Graham holding their leader at gunpoint, and you have the option to tell Joshua to let him go or kill him, with either choice affecting your karma and the ending. That said, not only did you mow down dozens of mooks to get to this point, but Joshua executes two kneeling-in-surrender White Legs himself.
In this case, it's less about saving the villain as it is saving Graham from his own rage. Salt-Upon-Wounds is stated to be doomed either way.
Iji completely averts this trope. How and which identical mooks you kill actually affects how the enemy sees you (though they do still all mostly attack on sight after the third level).
According to the logs, this may be because they still don't know who you're fighting for.
In fact, there is one specific faceless mook early in the game who has an effect on the plot near the end—whether or not you kill her determines whether in sector nine Iji will have a crisis of faith as she finds the log of a close friend of hers or find a log stating how the two of them found a safe place to flee to and will become two of the only three Tasen who are capable of surviving the end of the game. There will be no evidence at all that this mook was different from the others until you've reached sector nine (or more likely, read some of the earlier logs after reaching sector nine on a previous playthrough), and you have to infer which one she was. The mook in question is all by herself and little threat and can be easily killed or easily run past (and thanks to the truce won't attack you at all if you've followed the pacifist path up to that point), so it's probably a fair bet that most first-time players will kill her for her nano if they're playing a killer and spare her if they're playing a pacifist.
Iji actually apologizes after her first few kills. Her dialogue will also change the more (or less) she kills.
Averted in Fate's story mode in Magical Battle Arena. When everyone else fought their illusionary copies on the fifth stage, they felt uncomfortable about it because they were beating themselves up. Fate, on the other hand, felt really bad about it because they were still technically alive even though their lives were fake and temporary, which struck a little too close to home for her.
Averted hard at one point in Paper Mario: Color Splash. While on the Sunset Express, Mario meet a Shy Guy who delivers a brief soliloquy, pointing out to Mario that "every obstacle you've experienced has been the result of our hard and thankless work". While the Shy Guy seems to regret the life he's chosen, he knows there's no backing out of it, and notes that the next time he meets Mario, it'll probably be as an enemy. Later on in the game, after you defeat a specific Shy Guy:
In Marathon, there's no sympathy at all for the thousands of Pfhor you kill through the games (only one has been explicitly referred to, and that was as "that pile of chitin and fluids cooling on the floor behind you"). In the Marathon 3rd party scenario Rubicon, however, the player comes across a certain terminal after killing a whole lot of Enforcers. (The kind of mook seen in the picture.)
Infinity turns the But Thou Must! nature of the series and this trope on its head, at some points pitting you as a pawn in an internecine Pfhor power struggle cutting down Enforcers and Troopers alongside Fighters and Hunters, at other points as a slaver ruthlessly mopping up uncooperative humans.
In one of the early missions of Marathon 2: Durandal, you encounter a Sph't compiler at a terminal, who quickly notices you and is summarily dispatched. What was he programming? A message for you, apologizing for his incapacity to resist the compulsion to kill you, and forgiving your for your inevitable response. He encourages you to make haste and fight hard, for the sake his fellow Sph't, yet to be freed.
In Mortal Kombat X, both the Red Shirts and Mooks are slaughtered casually with nobody caring, not even the folks on the same side. The story opens with Johnny Cage making small talk with the helicopter pilot; who's decapitated minutes later like he was nothing. A fight with Scorpion later, Cage reacts to another soldier's decapitation with an "Ew!" and tossing the head aside. Later, Quan Chin kills one of his own soldiers just to get the attention of the Earthrealm warriors. Even for a game like this, it's pretty grim.
Lampshaded and statistically measured in Second Sight. Each mission gives you a "morality" score, which starts at 100% and drops each time you kill someone (but not when you trick one mook into killing another one). The player has the option of sneaking past some mooks, and most can be knocked out with tranquilizers. Oddly enough, fisticuffs are lethal.
The first Deus Ex has several instances where the question of killing mooks is mentioned. The most memorable instance, however, is in Paris where JC encounters a couple in a café. The couple are discussing the recruitment of their son to Majestic 12. When JC enters the conversation and makes his intents for Majestic 12 clear, the mother begs JC to keep an eye on for their son even though "those gas masks make them indistinguishable from each other". The whole game can be considered an example of this as well as it is possible to finish the whole game without killing a single mook.
Additionally, JC eventually defects, and the masked mooks he (optionally) slaughtered in the game's early stages become his allies. While some of them are to some degree humanized, the rest become, essentially, Red Shirts.
Deus Ex actually does an astonishingly good job of letting you choose whether this trope is in effect. Aside from a straight Pacifist Run, from the very start the game offers a variety of non-lethal ways to take out mooks, and up until you leave for the resistance your efforts to either cheerfully indulge in or stringently avoid wanton mook killing are noted by the game and commented on by other agents, for better or worse.
You get bonus experience in Deus Ex: Human Revolution if you avoid killing anyone save for bosses. You get even more points if you're never seen.
All three games feature hackable computers, complete with email messages to and from random, even otherwise unidentified characters that do much to humanize them - revealing bits of their personal lives, for example, or even that they have the same ethical concerns about their bosses as the player does.
One email series in particular in Human Revolution's "The Missing Link" DLC reveals that (1) the bad guys have a chaplain, and (2) said chaplain has been getting more and more visits from rank-and-file troopers upset and questioning the morality of what they've seen and done.
In Tenchu, the player can often hear the mooks utter some lines while hiding in the Shadows. That includes lines as "The doctor said I should stay away from dangerous business for a while" (said by a ninja of all people) and "I need to cut down on my drinking, or my wife will be mad at me again". Though that might not be intentional. You could feel sorry for mooks getting murdered seconds after saying "I'm sure tonight will be completely uneventful".
Valkyrie Profile: Covenant of the Plume plays with this - the protagonist (and by extension, his comrades) are actively encouraged to kill every foe they face, and brutally beat every trace of life from them while they're at it. The protagonist acknowledges what he's doing is morally questionable at best, but considers himself too far gone to care. Depending on the path the player takes, this can come back to seriously bite him in the backside.
The personal emails that you sometimes find, alongside useful passcodes, security information etc, in dead or unconscious guards' computers in Splinter Cell can be a bit of a guilt trip. In the first mission of Chaos Theory, one of the guards you can grapple and interrogate instead tells you how he knew something like this would happen ever since his family was killed by Americans, and how he's prepared to die so he can meet them again. And he doesn't even have a name. It's a little disturbing, actually; even Sam is creeped out. Averted in Conviction though.
Sin and Punishment has the Armed Volunteers, a military group devoted to defending against the monstrous Ruffians. Unfortunately, they're also creating martial law in Japan, so Achi's group labels them as their enemies. Once one of the main characters becomes a giant Ruffian, they mobilize, and the other main character's next mission is wiping out their entire military, a military that most of them joined specifically to protect humanity. If that wasn't enough, Achi laughs at their pathetic deaths, providing an early clue that there is something wrong with her.
Grand Theft Auto: San Andreas follows this trope in order to Follow the Plotted Line. CJ is told by some corrupt cops that if he leaves town, they'll pin the murder of another cop on him. Thing is, during the game you can murder cops and civilians by the dozens with your comeuppance being...respawning at the police station or hospital less 10% of your money.
Tenpenny and later Toreno stonewalls any attempts to put CJ away for good. And besides, it's knocking out a few fellow officers off the ladder.
No More Heroes 2: Desperate Struggle deconstructs this hard when it's revealed the whole plot is a revenge scheme against Travis for killing the Final Boss's father and brothers in a number of side missions where they appeared as mooks only discernible by their lack of hair.
There's also the Opposing Force expansion pack for the original game, where you play as a HECU marine. While said Marine is comatose for most of the original game and wakes up just as the military begins pulling out, your allies are all trying to work together to pull out.
Max Payne 2 plays with this; it is possible to overhear two mooks having a conversation about the theme park you're all in. One will even spoil the other, and the latter will get pissed at him. After that, they just stand there until you kill them or they see you. It's also possible to come across one mook playing a piano beautifully while the other watches. The two are part of a squad sent to kill everyone in the building, and the second they see you, both try to kill you.
The Enemy Chatter in the original game paints the mooks as actual people with lives and families — who just so happen to all be remorseless bastards.
Textbook use of this in The Force Unleashed. Using the dark side to kill hundreds, maybe thousands of stormtroopers fighting for their lives? Awesome! Trying to strike down Vader or Palpatine in anger? Bad apprentice! Bad!
The novelization does have the apprentice's pilot/love interest tell him that one of the TIE pilots he casually slaughtered was an old friend of hers, and killing's not so easy when you know who's under the helmet. But as soon as he apologizes she tells him that it's okay, she hadn't talked to that friend in years, and it never comes up again. Well, sort of. At one point the apprentice looks at Vader's plan to get all the rebel leaders in one place, which involved sacrificing thousands of loyal Imperials, and thinks that those lives mean nothing to Vader and the Emperor. Even though those loyal Imperials meant nothing to the apprentice either, and he killed a good percent of them anyway.
Vader said no witnesses. And seeing as how every single ONE of them will attack with the aim of killing you first, self-defense is hardly unjustified. To say nothing of the fact that the stormtroopers are genuinely on Vader's side, whereas to Starkiller they were either obstacles he was obliged to neutralize on orders of his master or genuine enemies, and that Vader and Palpy are quite capable of manipulating attacks on them to turn the tables (and the near-certainty that Palpy is playing possum) means that there is some justification for this.
With that said Vader himself is actually a known subversion of this trope. While he knows that his troops are expendable and can be replaced, he acknowledges the fact that they are actual people underneath their helmets. Hence why his Stormtroopers are so loyal to him, he is always fighting on the front lines with them, and he never orders them to do something he himself would not. Just don't, you know... fail him.
World of Warcraft subverts this with two mooks, one each for the Alliance and the Horde. When you kill the Alliance one, you find a letter on her corpse. Turns out she was forced to fight for the bad guys, was sabotaging them from the inside where she could, and she loved her daddy. Much the same applies to the Horde one, except the letter is addressed to his sister.
Mana-Khemia 2: Fall of Alchemy has Punis. They're capable of human language, thoughts, etc, and are friendly, gentle creatures; if you're playing Raze's path, you even get a party-member, a cute little girl, who was raised by Punis. Except Puniballs (not what you think... probably) are an ingredient in synthesizing, and how do you get those Puniballs? Why, killing Punis in random encounters! Including adorable Baby Puni, who have little pacifiers and everything. Might want to add that Punis look like blue Flan-type monsters, only with a happy little smiley face.
If you've seen the capabilities of Milo and Kate with the Project Natal technology, you won't be surprised to see this kind of thing happen in future games. The game demo has shown that AI can be programmed to be almost indistinguishable from a normal human, which could lead to some very poignant moments in a game: Talking to another randomly spawned ally in Call of Duty and hearing him give his views on the war or talk about his family, and then watching as a rogue grenade promptly takes him out. Or an enemy begging for his life after watching his squad get slaughtered and allowing you to talk to him just like you would a real man pleading to be spared. The humanizing aspects that modern AI technology is demonstrating could be enough to make you question senseless killing of the mooks.
Call of Duty: Modern Warfare 2 reminds one of this near the end. The Big Bad is then revealed to be a rogue general who has orchestrated the events of the game as one giant Batman Gambit, and now the two main characters shoot up his private guard in a mission to take him out for sheer revenge. While the game implies that these mooks are an elite paramilitary unit handpicked by the general and not really US soldiers at this point, there's no question that most if not all signed up believing they would be doing the right thing and probably aren't even aware of their boss's behind the scenes actions. On the other hand, Shepherd's troops saw him shoot Roach and Ghost, then threw their bodies into a ditch then doused them with gasoline. Although the Player is encouraged as Mactavish to treat them such a way when Shepherd bombs a base with many soldiers STILL INSIDE. And a variation of this occurs within the Airport scene, as most people treat the civilians as faceless, even though being encouraged to feel for them (and all the other people they have to kill). Some are dragging the bodies of their FRIENDS less than 20m in front of you.
This is probably one of the biggest complaints of new-to-MMORPG Star Trek fans about Star Trek Online. Since about 98% of the enemies in the game are members of other sentient species, and there are (at the moment) no alternatives to destroying them en masse, first-time RPG players often complain on the forums in a shocked state about the number of Klingons they just vaporized. The fact that several missions involve being tricked or manipulated into slaying innocents doesn't help in most cases.
The trickery runs you into What the Hell, Hero? territory when you slaughter a base of Romulans on the orders of an admiral who turns out to be a member of Species 8472. And any even mildly Genre Savvy player should have realized that by now.
In the web flash game series MARDEK, Emela asks this very same thing. She questions the morality of killing henchmen, remarking on how they have lives, and possibly families of their own, that she and her crew are tearing apart. She even exclaims "A killer killer is still a killer" (if you kill a killer, you're a killer as well), confusing the main lead. Her fellow teammates tells her to put it out of her mind, since as soldiers, this is part of the job.
However, it's also explicitly stated a few times that most of the monsters in the series are made of "Miasma" which randomly forms into monsters to attack you, and have no mind or soul. It goes on to say that this solves a whole lot of tricky ethical questions.
Although it doesn't come up in gameplay, in Metal Gear Solid, Snake's practically self-hating codec conversations reveal that he does take this trope to heart, although it is infused with some I Did What I Had to Do.
In terms of actual gameplay, this trope is reversed from Metal Gear Solid 2: Sons of Liberty onwards. If careful, it is possible to avoid killing or even being seen by any of the mooks in the entire game. Not so for the bosses, who must be fought and (in most cases) killed because it's necessary for the story to progress.
Metal Gear Solid 3: Snake Eater features a good aversion when you face The Sorrow - who, rather than fight you as the other Cobras did, makes you wade through a river occupied by the ghosts of every single person you've killed in the game up to that point, each one of them having injuries and making statements reflecting the method in which you killed them.note The bare minimum at this point are four enemies, namely The Fear, The Pain, The End and The Fury, as their bodies explode no matter what after their boss fights.
Before that, you can befriend the guard in the Groznyj Grad cells by throwing the food he gives you back out to him. He then shows you a photo of his family and tells you a little about his history. Unfortunately, Snake gets on bad terms with him after proposing the guard let him out.
In Metal Gear Solid 2: Sons of Liberty, each soldier has their own dogtags, having their name and info on it, and every different member has a unique one. Raiden become angsty after your first kill as well, feeling bad about it. You will even get called out on killing too many seagulls. That said, this is also the game that added the tranquilizer pistol, realistically allowing the player to complete the entire game, even the forced-combat sections, without killing a single person - except, again, the bosses that are scripted to die from their battle with you.
Kill enough mooks in Metal Gear Solid 4, and Snake will have a flashback to when Liquid accused him of enjoying the killing in the first game, and will throw up in disgust.
Metal Gear Rising: Revengeance takes a thorough look at this. Raiden establishes early on that he believes the PMC cyborgs he fights against made their choice to oppose him, and didn't deserve mercy for throwing in with the types of people his enemies were. Later, he's forced to face the fact that underneath their emotional inhibitors, many of the Red Shirt enemies he's been cutting down had no real choice at all, being manipulated by the same system he was trying to protect people from in the first place. Raiden is deeply disturbed by this. Jack... isn't.
Featured in Red Dead Redemption when bounty hunting. Bounties brought in alive give bigger cash and honor awards - but the bounty's gang of mooks are worth jack squat alive or dead. Which was often Truth in Television.
In Final Fantasy VII, the protagonists storm an underwater reactor under the city of Junon. They have to take the elevator to get there —and it's presently occupied by a girl, and two random Shinra mooks who are desperately trying to work up the courage to speak with her and ask her out. When they discover Cloud, though, they're bound by duty to try and stop him, and a brief battle ensues. The girl is horrified and laments the soldiers' death; Cloud and company don't even flinch. Similarly, another squad of Shinra soldiers tries to stop the invasion and scream "For Junon!" as they rush Cloud, and meet the same fate as their compatriots. The fact that Cloud himself was a faceless, nameless grunt a few years ago doesn't seem to bother him at all.
The Sonic series is actually generally an aversion. Robotnik's Mecha-Mooks (in most games) are actually Sonic's animal friends that have been brainwashed and put in a robot body, and by destroying their robotic shell the player is actually freeing them. The most straight-forward explanation for Gamma's story is that he becomes self-aware and targets his friends for this reason.
In Mega Man Zero, Zero stops short of killing the Guardians when you first fight them, with no explanation offered. Granted, you find out later that they're Hero Antagonists, but their subordinates, who are similarly just doing their job, are all fair game for bisection.
The Guardians also apply this as What Measure is a Red Shirt. In the second game, Harpuia chooses to spare Zero when Zero is at his mercy, even though he spent the previous game retiring Resistance soldiers left and right. Later on, they also let Zero leave with Elpizo after slaughtering his entire army.
The first two Thief games make a point of averting this. On the hardest difficulty you must never kill. Even at easy difficulty there are some major guilt trips awaiting the kill-crazy thief. Ironically the most effective of these is a spider. His name is Longdaddy, he is avoidable and the owner of the garden he lurks in is overjoyed at the work he puts in keeping his garden free from pests.
Lampshaded in Universe at War: the Novus faction has the Ohm Robos, dirt-cheap Mecha-Mooks who have a self-destruct attack. Their info card states that they know they're completely expendable... and they have no problem with the logic.
In Heavy Rain, one of the protagonists are given the choice of getting a crime boss you just interrogated his heart medication or leave him to die. Unless you're a really bad guy, you'll probably save him. On the way out you step over dozens of his guards, whom you killed on your way in. You might say they were shooting at you, but that's not an unusual reaction when someone drives a car into the house you're paid to protect.
This might qualify as Fridge Brilliance as it turns out that the character in question is the main killer of the game and is searching for a father willing to go to lengths to protect his son unlike his father over his late brother. And covering up events protecting his son is exactly what the villain in the scenario was doing.
Variation in Valkyria Chronicles: You get bonuses for killing the Aces, who actually do have names, but the game treats them like miniature boss fights and they have no lines. Then Selvaria's DLC came out and let you play as the Empire. The player character's face is never seen. This comes with a bit of a gut punch when you realize that you're playing as Oswald The Iron, one of the Aces that you probably gunned down with glee.
In one cutscene Welkin and Alicia come upon a wounded enemy soldier and tend to his wounds. He dies the next morning, but the enemy general who finds them decides to allow them to return to their unit rather than having his men shot them, as a sign of gratitude, even if their compassion had been in vain.
The Gallian military doesn't get that much compassion. Squad 7 is built on Video Game Caring Potential and the enemies have the above scene to remind us how they're human too, but the complete annihilation of most of the army proper doesn't have any attention paid to it except how tragic it was for the person who caused it, and how without the army, it's up to Squad 7 to save the day. A Million Is a Statistic, indeed.
Portal's turrets shouldn't invoke this, as they're just mass-produced robotic gun turrets. But their cute characterisation, saying things like "I don't hate you" when you knock them down made more sensitive players feel guilty, and that was before they start saying "I'm different."
Also, in Portal 2 they are said to feel very real pain, according to Wheatley.
"All simulated, of course, but real enough to them, I suppose."
Sengoku Basara plays this trope to the hilt. The various warlords you play as playable characters fight each other for practically no reason and are on quite cordial terms even as they're busy smacking the crap out of each other — the hundreds of people KOed every battle are never even mentioned. In one case in Samurai Heroes, Ieyasu consents to an alliance with the Hojo clan after the clan's messenger — the ninja Kotaro Fuuma — has butchered his way through Ieyasu's guards and doesn't seem to give it a second thought.
In MMORPG Runescape, this is parodied when in a quest cutscene an NPC guard openly acknowledges that the guards are killed all the time with no one complaining. His partner is horrified, at least until someone comes and kills both of them.
This is also lampshaded in the Vengeance! saga, to an extremely depressing effect. In the saga, you start off as following a party of adventurers that is working to fight through a dungeon. After fighting through the first room, the focus shifts, and you take control of one of the warriors they failed to finish off. This warrior is very pissed off because you killed her brother. She then proceeds to kill every adventurer in the party one by one.
Zig zagged in Super Robot Wars: original generation. Your battalion cuts through what amounts to an intermediate army of mooks without mention, then there's one that's portrayed as sympathetic, but he joins your battalion and you go back to killing an army of mooks without a second thought.
NieR: You will hate yourself when you learn what the Shades are.
Invoked on the player's part in Pikmin. Over the course of the game, you'll send wave after wave of Pikmin to their inevitable doom, and when they're gone you'll just pull up more without thinking about it. One of the songs released to promote the game, however, is a tearjerking, melancholy ballad from the Pikmin's point of view in which they're resigned to their fate.
We'll work together, fight, and be eaten,
But we won't ask you to love us.
Olimar, the main character of the game, shows shades of remorse as well. In his closing day remarks, he mentions how he feels bad about the fate that ultimately follows when Pikmin are left at the end of the day outside of the pod (they'll get eaten), and expresses outright guilt when all of his Pikmin followers have been destroyed, lamenting on how his absolute carelessness got his followers killed.
Guild Wars Beyond: Winds of Change - Having spent the better part of a decade at war, your character is increasingly bitter about the thousands he has killed and the pain it has caused to their loved ones and companions. One guard even muses he has spent so long treating a gang as a faceless enemy he never believed any would be there save to act as villains.
Seen earlier but not expanded on during the Nightfall Pogahn Passage mission. While disguised as a Kournan, it was possible to overhear the enemy talking about how Varesh was a visionary who planned to bring prosperity to all the nations. Most telling was one who talked about how his poor family had been promised fertile land in Istan for their role in the war.
Borderlands 2 parodies this mercilessly when you escort Claptrap to his ship and kill some mooks on the way -
Claptrap: Minion, what have you done? These were people...with lives and families - I'm totally kidding. Screw those guys!
There is also a weapon directly referencing the xkcdstrip that parodies this trope.
Spec Ops: The Line deconstructs this trope multiple times, seeing as your squad, well, massacres other American soldiers due to a tragic communication error. You can overhear some random conversations between enemies as they take breaks between patrols. Typically, they're sympathetic and even a little charming, and you're going to shoot them dead anyway because you're playing a shooter game. This is also invoked (to the point of parody) by The Radioman when your squad starts killing the last few soldiers guarding his compound:
The Radioman: (soldier dies) He was just three days away from retirement! (soldier dies) Well, there goes our fantasy football league. (soldier dies) He had...um...a dog? I didn't really know him that well. (soldier dies) Okay, you can have that one. That guy was an asshole.
Later, you come across a shrine to the dead, with their names listed on a wall. Additionally, one of your squad mates is crossed out, as he has been killed. The game simply leaves the wall in the room for you to notice it without ever calling it out, but if you look at the memorial, you can see the name and rank of every American soldier the protagonist killed up to that point. Ouch.
Dishonored averts this handily - not only are the guards humanized through idle conversations and letters, but there's actually a valid reason to avoid wholesale murder - the fewer city guards you kill, the less the city falls into chaos from the plague that turns people into ghouls (as the guards keep them in check.) Not even the main antagonists of the game have to be killed (though leaving them alive often involves setting them up for a Fate Worse Than Death.) Should you finish the game without killing a single soul, you'll be rewarded the "Clean Hands" achievement. Even the Weepers - people so terribly infected with the disease that they are little more than mindless zombies - count toward this, because in the best ending, a cure is developed to save them.
This is a minor theme in the 2013 reboot of Tomb Raider. While not apparent at first, later portions of the game show that the Solarii forces that Lara massacres her way through are regular people stranded on an island they can't escape, and do everything to survive—just like her. If you return to previous areas, to hunt for collectibles for example, you'll often find Solarii patrolling around and talking about, say, trading smokes for a book or looking for a pet rat called "Sprinkles" that has escaped one guy's pocket. What makes it all the more tragic is that these people can't be reasoned with and, more often than not, have to be killed to advance the game.
In Act II of Diablo III you can find a journal in the middle of a mook camp, in which one of the mooks writes about how long time they've been camping waiting for you, the stories he has heard about how strong is your player character, asking himself if they even have a chance to stop you, and wondering if they are not being used as cannon fodder by their superiors.
In Mass Effect you encounter a situation on The Citadel where you shoot up a bar full of mooks to get to a local crime boss. After clearing the first encounter, you go to the next one, where you have a choice of talking it through with the guards. You can explain that you just killed a roomful of people to get there and they should leave if they don't want to die too, instead of killing them.
In an early mission of Mass Effect 2, you infiltrate a Villain Team-Up in order to recruit their intended target, a vigilante who's been sabotaging their operations. The first half of the mission is spent peacefully walking among the mooks you will later turn on and kill, and you can even strike up a conversation with a handful of them.
In Crysis 3 after spectacularly blowing up a dam, you can find a black box next to the washed-up corpses of some enemy soldiers; Playing it reveals the screams and desperation of the soldiers trying to escape the flood, with their commander frantically ordering "Stay calm!", "Keep your head above the water!", and "Save your breath!". Suddenly the blowing of the dam doesn't look so awesome anymore. And if that wasn't enough, you can also encounter another group of soldiers whose Enemy Chatter reveals that they are there to rescue any survivors and their commander instructs them to separate the dead and resuscitate those who can.
In The Last of Us one of the reasons why the Hunters are hunting down Joel is to avenge their fallen friends.
Averted in a pretty unique way in Watch_Dogs, you can run a scan on any person you find in the game, including the mooks you face. It gives names, occupations, annual income, and little quirky facts about them you might be able to use to your advantage. Some are in fact family men who plan on picking their kids up from soccer practice once they finish their shift, or are going through a mortgage problem. On the other hand some are in fact wife beaters, affiliated with racist groups, and involved in child pornography, making gunning them down all the more satisfying. So in fact you can make sure everyone you kill actually is an Asshole Victim.
Star Wars: The Old Republic provides many textbook examples of this trope. There are a large number of cutscenes in which a villain falls defeated before the player character, who must then spare the villain's life if the character wishes to adhere to the Light Side. Killing the villain will move the character toward the Dark Side. And yet, wantonly slaughtering hundreds of low-level minions on the way to the villain is of no consequence, as far as the Force is concerned. In fact, going out of your way to slaughter low-level minions, as many players routinely do just to gain experience and loot their bodies for money and equipment, seems to be of no consequence.
Solas: We have fought living men, with loves and families, and all that they might have been is gone.
Iron Bull: Yeah, but... they were assholes.
Baldur's Gate: In the original game's Bandit Camp, you can listen in on the conversations the bandits have with one another. However, most of them literally amount to nothing more than them laughing at their own farts.
In Final Fantasy Tactics, there's a battle where you're fighting a bunch of squires. One of them remarks that they all "have families they would like to be able to go home to." You kill them anyway without a second thought.
Transformers: War for Cybertron and Transformers: War for Cybertron take a few moments out to, er, humanize the robots you encounter in the course of a mission, both on your side and on the opposing faction. While you could go in guns blazing into every encounter, waiting a while and playing stealthily will let you overhear things like Decepticons complaining about their faction's leadership, or Autobots wondering why some of the installations have No OSHA Compliance.
Flowey:"So you were able to play by your own rules. You spared the life of a single person. [lists off each monster] Think about those names. Do you think those monsters had friends? Do you think they had families? Each one could have been someone else's Toriel. Selfish brat. Someone is dead because of you."
If you kill Random Encounters after the Ruins but before Undyne, she will call you out for one of them.note Unless you killed Papyrus. That will really piss her off. Killing even a single monster makes Undyne unwilling to be your friend after you beat her, and killing one after becoming her friend leads to a rather dark ending.
The best ending requires you to not just avoid killing any bosses, but any random encounters as well. Killing a large number of random encounters but no bosses gets you roughly the same ending as killing their beloved hero (though most of the endings where you kill major characters are still darker than that).
Every monster, even the lowliest of slime monsters, has a personality and can be interacted with to end the fight nonviolently.
Several seemingly "random encounters" are unique monsters that only appear once, and you'll be called out by one of the bosses if you kill them. One random encounter is replaced by a friend who is "looking for [him]" if you kill him, and you later meet his father and in the pacifist route, his mother. Another monster only shows up once and is later revealed to have been friends with several of the bosses if you dig hard enough into side content.
The background comic for Ana Amari, Overwatch's support sniper has her thinking on the families of the Talon agents she is taking down, but mentally counters that with the fact that if she hesitates, her own friends die.
In FTL: Faster Than Light, if you come across a notorious Space Pirate and defeat his entire crew without destroying his spaceship, you may get an option of saving his life and getting him to join your crew, along with getting some of his loot. No word is ever given on saving his henchmen. Or all those other space pirates, rebels or obstructive bureaucrats you might have killed without second thoughts.