Subverted in City of God. One of the guards shot dead in a montage sequence has an adolescent son who witnesses his death at the hands of the heroic gang leader. The son joins the gang to take revenge and kills Ned at the end.
Parodied with great relish in the deleted scenes from the first Austin Powers film. All the henchmen Austin kills have families and friends, who are shown receiving the news of their deaths. One had a wedding coming up, and the other was happily married with a kid. The scenes were major Mood Whiplash, especially given the silly ways they died, which is probably why they didn't make the final cut. (For America, that is. They were in the UK/EU cut.)
In Part III, Nigel is able to defeat a mook by reminding him of how many anonymous henchmen he's indiscriminately killed over the years. The fact that he's not even wearing a name tag isn't improving his chances. Nigel just decides the guy is too pathetic to kill and orders him to lie down and play dead.
Road House: When Patrick Swayze's character breaks into the Big Bad's mansion, he beats the tar out of him, but then can't bring himself to kill him... despite having killed nearly all the villain's henchmen on the way in.
In The Chronicles of Narnia: Prince Caspian, the Big Bad is an evil, murderous, genocidal git who orders the killing of his own men for propaganda, and is generally not a nice guy. Three times the heroes have him at their mercy and either can't bring themselves to kill him or straight up let him go. Because it's wrong to kill. All those guards and soldiers who were just following orders get slaughtered by the hundreds without hesitation.
It should be remembered that there is a considerable difference between killing a soldier in a fight to the death, and killing an unarmed and helpless prisoner. Slaughtering Miraz's troops on the battlefield was the former. Killing Miraz when he could not fight back was the latter.
However the third time they had Miraz at their mercy was a fight to the death (those were the conditions of the duel between Miraz and Peter that both agreed to). Furthermore when both Peter and Caspian didn't kill Miraz, that enabled Sopespian to kill him and use that as an excuse for a deadly attack against the Narnians. It's likely if Peter had just killed Miraz, the Telmarines may have honored the terms and surrendered, especially since the conclusion of the honorable duel would've been seen by General Glozelle.
The Mooks in Equilibrium are no different from Preston before his Heel–Face Turn, drugged up on the emotion-suppressing prozium, and brainwashed their whole lives into believing that emotion was the cause of all evil, and wiping out "sense offenders" (people who feel emotion) is for the greater good. Pretend still guns them down without the slightest hestiation, and at the end, we see resistance fighters slaughtering them, even though by now they government they work for is already thrown down, and the protium factories destroyed. Had they lived just one more day, they'd be on the good guys side for good.
In On Deadly Ground, Steven Seagal's character brutally massacres dozens of guards on an oil rig, some of whom aren't even posing a real threat to him, ostensibly for the horrific crime of being accessories to pollution. After killing all these people, he finally gets the Big Bad right where he wants him, and then decides he's not worth killing (though The Chick then takes the initiative to off the Big Bad herself).
He more or less kills one for smoking (OK, smoking on an oil rig is not very smart, but blowing one up isn't either).
In Ballistic: Ecks vs. Sever, Antonio Banderas and Lucy Liu seem to spend most of their time killing either hired security guards or actual law enforcement officers, whose sole fault is that they unknowingly work for a corrupt official. The morality portrayed is quite questionable. One may be somewhat unsettled for the entire movie after the first shoot-out, and genuinely think it's building up to something more, but it never does.
Roger Ebert called out the film for the fact that we're supposed to sympathize with Lucy Liu's character upon learning that she's a mother, after witnessing her murder forty-some cops earlier on (who, no doubt, had families too).
Subverted and made into a plot point in The Machine Girl, where the heroine's slaughter of a squad of ninja mooks leads to a scene with their mourning families..
Occurs in the film Hitman, where the eponymous assassin has no problem shooting his way through hordes of gas-masked troops, but always lets named characters go, despite that fact that they are the ones leading the investigation into him. Particularly bad as the troops are simply ordinary Russian soldiers protecting their president.
Which is weird, since in the games this trope is inverted: 47 is supposed to only kill his target(s) and no one else. In fact, the Agency does not like it when innocents die and will send someone to kill an excessively homicidal agent if he continues the way he does.
When necessary, he will fight his way through security goons like that, but he just canonically doesn't because part of what makes him Shrouded in Myth is that his planning and skill are such that there are barely any witnesses to his assassinations or to his existence.
Star Wars tends to be subject to this trope, extending mercy to Darth Vader and his ilk while casually murdering his employees.
Luke and Lando destroy two Death Stars, killing all of the faceless mooks on them. It's unclear if any "innocent" people were killed (though the presence of entire detention blocks in the first, and the fact that the second was under construction and thus employing many non-combatants may cause Fridge Horror.) Fans of the films enjoy arguing about the morality of the acts, though the licensed franchise rarely goes there; one of the only examples is an issue of the 2015 Darth Vader comic in which a character directly mentions that many "great minds" were lost when the first Death Star exploded.
In between talking about the value of peace, the need for harmony and the murderous ways of the Empire, the Alliance spends a lot of its time killing Imperial soldiers and spacemen. (Good thing they're SpaceNazis!)
And almost all the species in Star Wars think nothing of blowing away a self-aware robot. That isn't even getting into the facts that the robots are essentially used as slaves.
As illustrated vividly in an episode of How I Met Your Mother, there are many fans of the early films who never realized that Stormtroopers were human beings subject to termination with extreme prejudice by the heroes. Possibly recognized by George Lucas who chose to replace them with silly (and somewhat stupid) robot soldiers in Phantom Menace.
Even worse in The Force Awakens. One trooper, FN-2187, decides to defect, free the Resistance pilot they had captured, flee with him and is given a name: Finn. He's one of the protagonists. Yet right after he explains that he was kidnapped as a child and brainwashed into serving the First Order, any and all subsequent Stormtroopers are standard Faceless Mooks that our heroes kill without a second thought, even Finn who, until a few days before, was one of them.
Discussed in Clerks, when Dante and Randall are talking about the thousands of innocent contractors that must have been blown up when the Death Star was destroyed. They are then interrupted by a man who works putting up drywall who tells them about how he was offered a substantial amount of money to work on a gangster's house. He refused, but let one of his friends know, and he took the job. Later, a rival gang pulled up to the house and murdered his friend and everyone on his team trying to whack the gangster - who wasn't even home. He does not say whether he warned his "friend"about the client's criminal connections.
Brazil has a major theme of the banality of evil. All of the mooks and Obstructive Bureaucrats are just regular people doing their jobs. When the heroes flee some dystopian police in Hot Pursuit, the police crash and the heroes cheer. Then one cop stumbles out covered in flames, flailing wildly. The heroes' smiles immediately wilt. Later, we see a pair of the cops take off their masks and gripe about their jobs like normal folks.
In Knight and Day, Tom Cruise knows there's one evil agent who framed him, and the agency now wants him dead. So Cruise actually manages to kill about thirty agents who were essentially duped into going after him but avoid directly killing the villain (though that's because he knows the MacGuffin will do it for him).
Judge Dredd has the title character kill dozens of law-enforcement officials, despite the fact that they legitimately believe him to be a murderer (and the likelihood that he personally trained some of them).
Subverted in that the only people Dredd kills are SJS, Internal Security troops who are on the paylist of the Big Bad and had no trouble killing innocent witnesses.
While Merantau does not explicitly confirm the mooks' deaths, the protagonist uses a number of techniques that would almost unquestionably kill, notably kicking a man in the head in the middle of a running long jump such that his body is sent flipping backward and whips his skull into the corner of a steel shipping container.
However, seeing as how said mooks were all willingly participating in human trafficking and slavery, it's somewhat difficult to feel sorry for them.
The Matrix films, particularly the first film, has this happening in spades to the human security guards and law-enforcement officers.
Pointless Waste Of Time pointed this out in a critique of the Matrix, painting a mental picture of an aging, underpaid security guard who can barely afford his wife's arthritis medication, suddenly gunned down by a group of leather-clad murderers with whom he had no quarrel.
Perhaps made even darker when you consider that said invincible Agents, when their circumstances are less dire, make a point of protecting human agents of authority-if only because they work for them, and law and order is fundamentally important to keeping the populace from dying in inconveniently large numbers.
At the end of Batman Returns, Batman pleads with Selina Kyle not to kill arch-villain Max Shreck, and to let Batman take him to the police instead. This is perfectly in keeping with Batman's typical policy against using lethal force... but not his behavior throughout the past two movies, in which he has killed or at least maimed numerous henchmen.
The Operative in Serenity is a subversion-he respects all human lives including those he takes, which is any he deems necessary for his cause, be it his own mooks or even children. The only time in the film he is ever angry is after Mal pulls a stunt that gets hundreds of Alliance mooks killed. When the Operative tells Mal that a lot of innocent people died because of what he did, he shows a similar respect for anonymous combatants, replying "you have no idea how true that is" in reference to the Reavers, who were innocent people themselves before the Alliance made them what they were.
Subverted in The Assignment by virtue of the lead character's attitude. He is extremely upset that he has had to kill American agents, which is understandable considering he's on their side.
Ian, the Big Bad of National Treasure, is badly shaken when one of his mooks dies. When Ben tries to make him see going on will risk more lives, Ian harshly tells him none of their lives are worth more than Shaw's.
G.I. Joe: The Rise of Cobra: Vipers and Neo Vipers are mind controlled drones. Granted the Joes don't know about this, but combined with Destro's plan for Duke who is to say he is the first unwilling recruit?
Hornets' Nest: After stabbing, shooting and blowing up random German soldiers left and right, even shooting one who is wounded and trying to get up, Turner makes a big deal about sparing the life of German officer Captain von Hecht.
Subverted humorously in Iron Man 3-Iron Man, while charging through the baddie's mansion, aims to shoot a guy, but the guy just puts up his hands and says "Honestly, I hate working here. They are so weird."
In X2: X-Men United, the X-men, particularly Wolverine, slaughter countless random commandos yet spare the life of Big Bad Striker. Wolverine also kills Lady Deathstrike, who was Brainwashed and Crazy just like Nightcrawler was.
Generally played straight in Ant-Man, wherein plenty of suit-wearing Mooks get knocked out and left behind to die in Cross' building when it implodes (along with any civilians, cops, etc. who might have been in there). However, in one aversion, Luis makes a point of going back for the guy whose clothes he stole. He gets him out of the building in time, risking his own life to do so, and even ensures he gets medical attention. (To be fair, that mook never tried to attack Luis.)
Kill Bill has Bill force the Bride to acknowledge under truth serum that she's been and always will be a killer. And that the dozens of people she killed to get to him felt good to kill, which she tearfully affirms.
Moonraker. Although Bond does kill the main villain, the film's secondary bad guy, Jaws, changes sides at the last minute and receives redemption. Meanwhile it is strongly implied (yet pointedly never directly shown on screen) that Drax's "master race" specimens, whose only crime it seems was to be genetically perfect and be on his payroll, are either slaughtered by the US troops who invade the station or are left to die as it breaks up. Keep in mind that this would have also likely included Dolly, Jaws' cute and kind girlfriend (but technically a mook - she even wears the "yellow suit of death") had he not changed sides.