Ruthlessly subverted and taken apart in Hench, by Adam Beechen and Manny Bello. In this graphic novel, a professional henchman (he's worked with a lot of supervillains, and tells us which are good bosses and which ones to stay away from at all costs) reflects on his life, and how it got so crazy. He isn't in the life For the Evulz so much as having no other way to make a living and support his kid.
Volume One, Issue Twelve of Grant Morrison's The Invisibles, titled "Best Man Fall", is a Posthumous Character study of a guard who appeared in only one panel of a previous issue. It shows various snapshots from his life, up until the point where he gets shot. While he's far from the a saint, it still works to make you feel sad for him dying.
This ends up being one of the running themes for the series, where mooks are often depicted as something more than grunting savages with guns before getting gunned down by the heroes. Yeah, it starts to wear on them, too.
One of the many Star Wars comic series, called Empire, focuses on the Empire's side of the conflict against the Rebels. One of the main characters is an up and comer in the Empire who gets mocked because he cares about the lives of each and every Stormtrooper.
In FrankMiller's The Dark Knight Returns, Batman won't kill the Joker even though his grinning adversary has recently murdered a studio full of people, on live TV. Earlier on, however, he has no hesitation about using a gang member as a Human Shield, and then turning that gangster's machine-gun on his buddies. Sure, the gangsters were bad but WTF, Millar?
That was a split decision to save his own life. The Joker was already beaten. Just to be safe, Batman applied enough pressure to paralyze him from the neck down.
One of the last few G.I. Joe comic books ("America's Elite") had a flashback to the early days of G.I. Joe and the evil Cobra. One of the undercover operatives was saying (paraphrased) "Yes, General Flagg, some of them are jerks but a lot of them are just confused people, they aren't really bad."
The subject is explored in the Astro City arc Dark Age when Royal and Charles go undercover as mooks in Pyramid.
This trope is brought up sometimes in Sin City, despite the protagonists' violent nature. Marv refused to kill the initial set of cops sent against him and he employed similar methods when deaking with the henchmen at the Lord's estate, Wallace only killed a few assassins since he was one of the few SC characters who didn't like killing, Hartigan killed the guards at the Farm but mentioned that he hated doing it, and Dwight once questioned whether or not he should kill a cop on the grounds that he might be one of the few honest ones.
In the most recent Wolverine comics, one issue explores the background of a female Hand ninja, known best for being Marvel's go-to mooks for stories set in Japan. The ninja dies early on during one of Logan's frequent rampages. The Hand brings her back to life only to serve as the human equivalent of a broodmare. She refuses and instead joins the Right Red Hand, a group of people who blame Logan for ruining their lives.
One issue of Tales of the TMNT goes into the backstory of a new recruit to the Foot Clan ninjas—his family, his personality, and why he wanted to join the Foot. He comes back from his first fight with the turtles in a body bag.
Fables loves to subvert this. We see bits and pieces of the Emperor's forces, background, interests, beliefs... Boy Blue while he is sneaking through the Empire gives the goblins he questions the chance to surrender when he confronts them since he just wants information. (Not his fault they kept attacking him.)
Transformers IDW comics had both types of Aversions. There was a group called the Machination, where Humans would have themselves augmented into Transforming robot heads, and control giant robot bodies. When the Autobots fight them, they only stun them or cause them to crash, despite the fact that they've tried to kill the Autobots several times, almost killed Ironhide, and painfully took apart Sunstreaker. By Maximum Dinobots, The Monsterbots and Dinobots, being the most violent of the Autobots, gleefully kill, dismember and even eat the Humans, and are only stopped from killing their leader because Ultra Magnus wants to arrest and try him for crimes on many other planets.
Transformers: More than Meets the Eye: The Decepticon Scavengers (six Mauve Shirts) discuss this trope, during one battle, where Optimus and Megatron shut themselves off and plugged into a neural network. They could see the battle from the eyes of all their troops, and used it to better coordinate their attacks, The Scavengers say troops were reduced to numbers and statistics, and at the end of the day, the only thing separating the sides were that the Autobots had the decency to collect their dead while the Decepticons left their troops corpses to decay.
Here's a notable example where this happened as a result of a Red Shirt dying. The first time Spider-Man villain Venom escaped from the Vault, he had to kill a guard to do so. (Even then, the guy's name was mentioned, as was the fact that he may have gotten the position by a rich relative who thought it was a high-paying easy job.) Much later, the guard's rich father and several of his friends sought revenge, forming a vigilante group called the Jury, equipped with high-powered armor based on the technology used to build the Guardsmen suits at the Vault. Unfortunately, they quickly turned into the Knight Templar type, and even put Spider-Man on trial in a Kangaroo Court, blaming him for creating Venom in the first place. It was actually a ploy to guilt him into agreeing to help them get revenge against Venom; but when he realized they planned to murder him, he came to his senses and beat them all senseless.
Kyon averts this trope in Kyon Big Damn Hero. Before fighting 24 Mooks with Yuki's help he asks her not kill any of them and/after the fight, worried about the battle aftermath on them, he asked her how much they were injured.
The Villain Protagonist of the Mass Effect fanfic The Council Era, Tyrin Lieph, completely disregards his own Mooks as expendable. While this is reasonable when it only refers to his Mecha Mooks, later within the storyline, (i.e. The second part, The Krogan Rebellions, tenuously scheduled to start in summer of 2011) he has completely disregarded the value of the lives of his dezban militia, the Krogan Resistance Movement, and his own devoted Soldiers of Salvation.
Subverted, in The Stalking Zuko Series Aang is called out on sparing Ozai when he and the Ocean Spiritnote although it can be argued that the Ocean Spirit was the one in control at the time slaughter countless of Fire Nation soldiers in the Siege of the North.
In Perfection Is Overrated, this is played with with regards to the First District minions whom the Usurper-possessed Obsidian Lord and his entourage killed. It's pointed out in the author's note, and in one such minion's final moments that they leave loved ones behind. However, it's also pointed out that The First District was a secret organization, so they were also most likely willing participants, and performed immoral or illegal deeds in the course of their duties. The note concludes that the slaughtered minions are "not necessarily bad people, but they made bad decisions; whether their deaths are a fair consequence is another matter, but they came as a result of their own actions."
Sonic the Hedgehog 2: Special Edition reveals that one of the powerups from Oil Ocean Zone was sapient. His name was Failure Cresh, and he had a thorough backstory involving being born with a ten-ring monitor for a head, and a Hilariously Abusive Childhood resulting from this. When the player destroys the monitor, the video pauses for a moment of silence—but it's obvious that the player himself is completely oblivious to the fact that he just killed a person.
The characters in Darwin's Soldiers kill a lot of terrorists, rogue guards and other assorted Mooks and no one seems to have a problem with it.
New York Magician: Part of the reason Michel hurls Malsumis off a building is because he's pissed off about Mal's cavalier attitude towards his minions' deaths, and the mortality of humans in general, culminating in "The Reason You Suck" Speech.
Touched upon in the Star Wars canon; the Stormtroopers were indeed mourning, but it was less "terrorist attack" and more "disastrous military operation". However, the Stormtroopers were able to channel that mourning into devastating fervor during the Yavin base ground battle and avenge their fallen brethren.
There is a Real Life protocol or general custom in war to not target the enemy Head of State (even though he's in ultimate command of the enemy war effort, and even if he might bear full responsibility as political originator for the enemy aggression if his country is the aggressor).
This Real Life common Karma Houdini tendency for the masterminds, profiteers, or political agitators for war, is commented on in a few protest songs, such as Bob Dylan's "Masters of War", and Black Sabbath's "War Pigs". From the latter:
Fair game, but often had an enhanced chance of survival, because it was frequently much more to your benefit to capture kings and princes and sell them back for ransom than to kill them, and then deal with their successor and the international grudge you'd just attracted.
Notably, this is not actually a law of war. According to the Geneva Conventions, the enemy's high command is fair game for targeting, up to and including targeting the commander-in-chief for assassination or bombing his house.