Taken up to eleven in Michael Crichton's final novel Pirate Latitudes. The "heroes" slaughter hundreds of people, among them a nineteen-year-old kid. It's not even acknowledged that the mooks these people slaughter are actually on the side of the law and it's the protagonists who are menacing the populace. The Big Bad of the novel is essentially evil incarnate, because he'd have to be, in order to be worse than the heroes. This novel was published posthumously, and it wasn't actually complete.
In Eldest Eragon does some angsting after killing rabbits to eat them and resolves not to eat meat anymore because it involves killing living things. (Let's not start on the Fridge Logic of a young man raised as a medieval peasant being squeamish about dead animals.) This does not prevent him from later in the book massacring enemy Mooks in a borderline Ax-Crazy manner, even after the opening to Eragon establishes that most of these mooks just got picked up by the draft, and some may even be from his home town.
It gets far worse in Brisingr. When Eragon is undercover in the Empire with Arya, they get into a fight with a group of soldiers, they kill them all with no weapons. One almost escapes, and as Eragon catches up with him, starts begging for his life, repeating (truthfully) that he was dragged against his will into the war, that his parents will miss him, that he has yet to get married and live a life, and so on. Eragon rationalizes him as a threat, and breaks his neck with his bare hands. What the Hell, Hero? To be fair, you can argue (and people have. Extensively.) about whether any of the other options available to Eragon (memory-wiping, invisibility, knocking the man out and leaving too quickly for an alarm he raises to make a difference, or trying to recruit him to La Résistance and sending him elsewhere) are really viable here. But the real point is that Paolini doesn't. No indication is given that avowed vegetarians Eragon and Aya think twice before slaughtering effectively defenseless punchclock villains, even when they're surrendering.
That scene lampshades this trope. Arya and Eragon discussed beforehand how many servants are charmed to serve and follow the empire, and releasing them would just force them to tell the truth back to the empire.
The trope is later played with when they attack a major city. Eragon knows that many of the troops are not charmed and compelled to follow The Empire, so he offers them a chance to surrender beforehand, as many fear fighting a Dragon rider. Many of them do, and he asks his allies to treat them well, as they willing fully surrendered. The ones that don't proceed to fight and are killed by Eragon.
Subverted with Eragon's cousin Roran who, by contrast, is uncomfortably aware of the humanity of the soldiers he kills and often has to remind himselfwhere his priorities are. Eventually, Roran goes into the kill or be killed mindset of the war.
Played With again when the battle commences at the end of Brisingr. The enemy Mooks are poisoned, and killed without mercy. Eragon goes into a frenzy of slicing through enemies in the war. When all the action is over and the enemy retreats, a weakened and physically drained Eragon wanders around the battlefield, healing Soldiers of minor to fatal wounds, and not caring about their alliance.
Yes, a good swipe at head height would kill... ...some mother's son, some sister's brother, some lad who'd followed the drum for a shilling and his first new suit. If only she'd been trained, if only she'd had a few weeks stabbing straw men until she could believe that all men were made of straw...
It's also the original basis of the City Watch characters: Guards! Guards! is dedicated to the mooks:
Whatever their name is, their purpose in any work of heroic fantasy is identical: it is, round about Chapter Three (or ten minutes into the film) to rush into the room, attack the hero one at a time, and be slaughtered. No-one ever asks them if they wanted to.
The Star Wars Expanded Universe novel Death Star features the personal lives of many mooks. For example, one of the guys seen at the fire control station of the laser is there, as is the Stormtrooper who leads the chase against Han. Due to an influx of guilt and a bit of Force sensitivity, many mooks form an escape plan just to get out of the damned place.
The Buffy the Vampire Slayer 'Gatekeeper' novel trilogy. The Big Bad has dozens of human mooks on his side. Many of them are smart enough to figure out they're getting a raw deal from a guy who wants to turn Earth into a charnel pit. The authors delve into the minds of many mooks, making some sympathetic. Then the mooks tend to explode.
There's also the fact that orcs are never shown even trying to surrender- if they're losing, they always either run or fight to the death. This rather limits one's options in dealing with them.
Inverted in The Dresden Files, especially near the end of Small Favor. Harry is more than willing to do absolutely everything in his power to kill Nicodemus, even slowly throttle him to death over several minutes, but he steadfastly refuses to kill the mooks that chase him down afterward.
In The Well of Ascension by Brandon Sanderson, Vin is perfectly happy to attack an enemy keep, killing dozens of soldiers at least. However, when she reaches the lord and his son — the only two named characters in the building — she refuses to harm them and leaves instead.
This is actually a subversion - it wasn't the sight of the lord and his son, but the realization that the lord was crippled, the son was harmless, and though the lord had made himself look very dangerous, he wasn't a serious threat that did it - because this makes Vin realize that she just killed a building of people for no reason. She promptly goes off, sick to her stomach, and hides until her friends find her.
Played straight with Kelsier from the same series. He considers working for the nobility, even if you're just a Punch Clock Villain, to be a death sentence. However, Kelsier is generally presented as bordering on being a Well-Intentioned Extremist (albeit not outright villainous).
Jenna in the Great Alta Saga is prone to these moments, but she usually feels guilty (read: can barely keep going) afterword. It makes sense given that she has been raised in a culture that has no real taboo against violence, but she remains a seventeen-year-old girl.
In Aaron Allston's Galatea in 2-D, the hero tortures one of the villain's mooks to try to get information from another. He slackens off without getting everything he wanted, realizing that she didn't know anything and that he was invoking this trope. That thought horrifies him — just because they weretwo paintings who came to life, and whom the villain had sent to kill him didn't mean torturing them was all right. At the climax, the trope is reversed: they kill the villains and tell the mooks that as long as they stay out of their way, the heroes won't bother them.
Surprisingly (given the nature of the series they spawned) often averted in the James Bond novels. Bond almost never kills without considering the consequence, even in Dr. No he actually has to tell himself that the two nameless security guards he is about kill were almost certainly murderers themselves. Also, the start of Goldfinger shows Bond in depression after assassinating a mexican drug lord.
In His Dark Materials, this is a function of the daemons: if the daemon is a rare animal, it would be a crime to kill the owner. If the daemon is a guard dog or a wolf, go ahead it's a war, any kill in the other camp is good!
It's also played straight. Even after the Animorphs start to think of the Hork Bajir and Taxxons as people they are still far less likely to look for nonlethal resolutions than they are when dealing with Human Controllers, although is't somewhat understandalbe, since a human is much easier to incapacitate non-lethaly than a huge blade-covered lizard or an (also huge) ravenous centipede.
Which is itself brought up as a plot point when Visser One figures out that the Animorphs are human because of this. It's probably safe to say that this trope was deconstructed.
In one of Michael Moorcock's Elric stories, not known for their kind treatment of, well, anyone, up to and including the human race, there is a subversion where, after a humble sailor and a central character have been killed, Elric carves a memorial to the latter, and the story then comments on how there are no memorials made for the former (I think this was in "The Jade Man's Eyes").
Nnedi Okorafor's Who Fears Death. The heroine refuses to kill the villain when she has him at her mercy, despite the fact that he has been leading a genocide for some time now and plans to continue to do so (she claims to oppose killing when faced with this choice). She shows no remorse when she kills and/or blinds large numbers of random nameless people, though.
Averted in Percy Jackson and the Olympians. Percy kills countless monsters, (and it's not exactly killing because the monsters can reform) but when a demigod apart of Kronos' army is fighting he will do whatever he can not to kill the demigod. Although he doesn't appear to mind killing enemy human mercenaries.
R. A. Salvatore's Demon Wars Saga largely follows this trope with regards to goblins, giants, and powries (evil dwarves), with one interesting exception: in Transcendance, the heroine Brynn and her elvish escort come across a band of goblins deep in the wilderness, away from any human settlement. The Elf almost casually slaughters the goblin group, but Brynn objects, claiming that the goblins have done no wrong and do not deserve to be murdered. The Elf's response is rather disturbing (he holds Goblins collectively responsible for atrocities committed by their race in the past), and the whole thing ends up never getting mentioned again in the series.
Inverted to the extreme in Ken Follett's Lie Down with Lions, where Jane refuses to kill the Russian soldiers who are at that very moment trying to capture her and Ellis and bring them back for execution, and who are at war with the very Afghans who's she's been trying to help for the past few years, because the soldiers "all have mothers." She has considerably less consideration than that for the actual Big Bad.
Star Wars, at least with regards to certain types of mooks. In one novel, during a scene from the perspective of an Imperial officer, he muses that since the Emperor's death, stormtroopers are even less willing to retreat, becoming almost fatalistic in their outlook. Said perspective also includes musing that stormtroopers aren't really people—even the Empire believes that, apparently. Meanwhile, it's averted with the more run of the mill mooks. In the Wraith Squadron novels, they try hard to avoid casualties, since they're fighting more for hearts and minds than control, as the New Republic has already conquered Coruscant. One sequence a gunner jump from his ground-based gunnery tower a second before a Wraith fighter hits it, and he muses that at least he won't have to worry about the outcome of the battle in another fifteen hundred meters. One thousand. Five hundred...
Averted, sometimes, in The Tomorrow Series. Ellie often reflects that many of the enemy soldiers she shoots, blows up, or runs over with big vehicles are young people not that different from her and her friends... but by the end of the series, the protagonists are so hardened that they ambush and kill enemy patrols just for something to do.
Redshirts explores this, as the mooks are the main characters.
Strongly defied in the Babylon 5 novel To Dream in the City of Sorrows, where Sinclair, the newly appointed head of the Rangers addresse his new subordinated with a speach wherein he stresses that the goal of Rangers is protection of life, all life, even that of their enemies, the Shadows, so those who'd joined the Rangers looking for revenge against them, might better leave right then, for they would not find what they are looking for.
Shadow Children: The sixth book has a group of Population Police officers killed, and their survivor shanghai Matthias into an escape. Instead of kidnapping him, the officer, Teddy, thinks he's saving the boy, and even explains why the Population Police were a good idea in the first place. Teddy goes onto to take him to HQ, and introduces him to the other agents, who're all quite friendly and easy going. Matthias is torn, as the police agents who've hunted him for his entire life, are just like regular people doing what they think is right. Teddy later dies handling Poison ID cards, and a memorial is set up for him.