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 cut.)
In Part III, Nigel is able to defeat a mook by reminding 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. The guy just decides 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.
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 not very smart, but so isn't blowing one up)
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.
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.
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.
Rationalized 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 felt bad about his friend dying, but doesn't feel sorry for him, as he knew exactly what he was getting into, and says that the same would apply to the Death Star workers.
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 completely innocent agents but avoid directly killing the villain.
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.
In Goldeneye, James Bond kills a number of Russian soldiers while he and Natalya are escaping from the archives, despite the fact that they're only shooting at him because they think he'd stolen the Tiger helicopter and killed Defense Minister Mishkin.
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.
Pointlesswasteoftime.com 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 & order is fundamentally important to keeping the populous from dying in inconveniently large numbers.
Averted by The Wizard of Oz in that none of the guardsmen are even seriously harmed when Dorothy and company break into the Wicked Witch's castle. In fact, the guardsmen are thankful when Dorothy destroys the Witch and breaks whatever hold she had on them.
They're Winkies, and they're supposed to be enslaved, as explained in the book. (But see Wicked...)
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.