Inverted with great style in Samurai Jack's 50th episode, "Tale of X9". X9 is a retired assassin droid who, thanks to an experimental emotion chip, has fallen in love with a puppy. Aku kidnaps the puppy and forces X9 to go after one last mark — Jack. The episode is completely from X9's point-of-view, with Jack only making an appearance right at the end. You know X9 is doomed, but you root for him none-the-less. This has got to be the only time you feel sorry Jack won a battle. It is arguably one of the saddest, best episodes of the entire series.
And while he does slaughter Aku's minions without remorse, he's at least consistent in that he'd gladly kill Aku himself, should he get a chance.
It does help that the majority of Aku's minions are robots.
In Ben 10, the trope is most obvious with the Forever Knights. Because they wear face-concealing armour, it's okay for them to be left in a Collapsing Lair or caught in a nuclear explosion. This is only the most obvious instance.
Lampshaded, parodied, and subverted with almost sadistic glee in any scene in The Venture Bros. involving Brock Sampson and the Monarch's minions.
A big subplot in the season four premiere involved one of the minions trying to find some way to bring his friend back to life, first by trying to get him cloned by Dr. Venture, and then tried to get the Necromancer to use magic. Dr. Venture refuses the payment (a comic book), because he deems it worthless (it wasn't, but by the end of the episode, it was). And it turns out the Necromancer can't actually do necromancy. Despite trying to raise the eponymous brothers in season 2's premiere and admitting he's done "hundreds" of them. David Blaine and Evel Knievel for example. As was Ronald Reagan until he bounced a check.
Although with Orpheus, that may have to do with those bodies were whole, whereas Henchman 24 was blown to several pieces from a blast of plastic explosives.
Ĉon Flux played with and subverted this trope time and time again. After the very first short, which showed Aeon mowing down endless armies of mooks, the second short focused on the aftermath, sympathetically showing the deaths of two of her victims and also (briefly) showing a mop-and-bucket mook whose job was to clean up the lakes of blood left behind. A later short ("War") pushes the trope even further, showing a Heroic Hero slaughtering endless mooks until one mook proves to be an even more Heroic Hero. The new hero kills the last hero and the plot quickly switches sides. This pattern repeats itself four times.
Two episodes of G.I. Joe features interesting aversions, in which what would normally be a Mook was presented as very human:
In the first one, Slip-Stream was forced into a very one-sided Enemy Mine situation with a female Cobra Strato-Viper, after both crashed in the wilderness and ended up in an abandoned COBRA base, one which had actually been evacuated because one of Dr. Mindbender's failed experiments - a huge, slug-like monster - was lurking inside. The Viper was certain for most of the episode that her comrades would come to send aid, but all that eventually came were a bunch of Battle Android Troopers who didn't help her at all (which the beast tore through quickly) and eventually, a message from Mindbender himself confirmed the worst - she wasn't considered important enough to rescue. Fortunately, the Joes were more willing to rescue Slip-Stream, and got both of them out. When Lifeline asked him if he had brought a prisoner, the Viper slowly tore the COBRA insignia off her uniform, and Slip-Stream responded, "No, I think this one's a recruit."
The second example was the episode where the Joes tried to salvage the sunken FLAGG aircraft carrier, only to be interrupted in their efforts by Zartan and the Deadnoks; however, both factions find that the sunken vessel has been taken over (more or less) by a former Cobra mess sergeant named BA McCarr, who went down with the vessel and managed to survive, but at the cost of his sanity. Zartan can't even remember him, but when he appeals to the former Cobra chef claiming that he's a member of the organization, BA is surprised that Cobra is still around, and very angry that they never tried to rescue him. Later in the episode, BA suffers a blow to the head that knocks some sense into it, and he helps get everyone to safety, but when Zartan offers to take him with them, he angrily tells him off and disavows Cobra. ("I don't want to go back to Cobra!" he cries. "They left me to drown!") The episode ends with the assumption that he also defects to the Joes' side.
Involuntarily inverted in the first two seasons of Teenage Mutant Ninja Turtles (2003): thanks to standards and practices, defeated mooks were invariably shown as being merely knocked out, despite the fact that the turtles theoretically had no problem killing in self defense and tried several times to kill the Shredder. (And by "tried", we mean "decapitated him".)
In ReBoot, Matrix slaughters countless viral Mooks and numerous viruses, but after a huge battle, he spares Megabyte, despite his torturing Phong, oppressing the people of Mainframe, infecting many of the survivors, and turning Mainframe into a hell hole. At the very least, Megabyte comes back to bite them in the ass because Matrix didn't just put a bullet in Megabyte's face.
In Matrix's defense, Megabyte did give Enzo a kickass guitar for his birthday.
Averted in the episode Game Over, after blowing away a huge chunk of Megabyte's forces who were clumped up into a kill zone, Dot dejectedly says "Well done, people." before walking off to cry. She goes on to celebrate with her staff, but she's pretty much just putting on a face.
Stroker and Hoop. Hoop fires at ninjas in order to save Stroker and his son. Instead of scaring them away (his secret usual M.O.) he nails one in the brain. Hoop goes into a wild emotional breakdown and essentially takes over the ninja's life. Stroker doesn't see what the big deal was (he intentionally shoots people all the time) and the ninja's boss kills his own minions (despite saying how stupid it would be to do so).
For all that Avatar Aang struggled with the morality of killing Ozai, he never gave much thought to the soldiers he blasted off the mountaintop in "The Northern Air Temple" or all the engineers and technicians drowned in slurry in "The Drill". Or even the crews of the ships drowned when he fused with the Ocean Spirit.
Also, while the finale was spent with Aang figuring out a way to not have to kill Ozai, during the battle Sokka figured out a plan that completely destroyed The Fire Lords fleet of airship, killing about 300 soldiers offscreen.
Megatron's Decepticons in Transformers Prime are—save for a few lieutenants—seemingly nameless, faceless Vehicons (unlike most characters on the show, they have Cylon-like unemotive faces). The Autobots kill them by the dozen in each episode, and Starscream once demonstrates a Doomsday Device on a hapless Vehicon. But...later on we see them talking, interacting, and some even expressing doubts about the current leadership, demonstrating that they are living thinking beings. Yet, average, about 10 of them die in every episode at the hands of our "heroes", often in very brutal ways (disemboweling, decapitation) which is allowed to be shown on a kid's show because, a) it's Hasbro's own network and b) "Hey, they are robots". And all this often by the very same Optimus Prime who offers Starscream to actually join the Autobots, and for a long time, does not want to kill the Megatron who essentially destroyed Cybertron and turned it into a desolate world crawling with cyber-zombies—because they used to be buddies...
Utterly averted in the 2011 Thundercats show. The lizards, while being ancient enemies of the thundercats, are revealed in the first episode already to have a very good and valid reason for attacking Thundera - the cats have occupied the most fertile lands in the desert and are denying other races the food and water needed for survival. Despite the lizards remaining the main antagonists throughout the first 13 episodes, many lizards have been depicted as individuals, despite most of them remaining nameless. The best example are the two lizard prisoners whome Lion-O saves from a lynching mob in the first episode—at the end of the second episode, the same lizard repays his kindness by helping him escape from prison.
Panthro is very much an equal opportunity guy in his handling of the trope—his own arch-enemy gets the same treatment as any nameless mook. Whenever he encounters Grune, he doesn't even want to talk to the guy who used to be his friend before his betrayal—he just wants to kill him, same as any other enemy. (And, he is not afraid to make any sacrifices to get the job done).
TRON: Uprising: Averts this. Beck, the protagonist, has a no-killing policy, sparing guards, or stunning them. In the first episode, him not killing a guard gets that guard to help him out at the end. In the Scars two-parter, Tron witnesses where the guards come from, regular programs being brainwashed, and later, a different guard saves his life and fakes his death.
Other characters, like Rilo, Cutler and even Tron himself, have killed when put in a life or death situation.
Parodied in the American Dad! episode "The Boring Identity". When the CIA raid a Doug & Busters after receiving intel that the real Osama bin Laden had been working there as a manager, they brutally kill the innocent workers who are just doing their jobs, but they take Osama alive.
In another episode, Stan is tricked into robbing a museum by his father, and a scene in which he viciously beats an elderly security guard has excerpts of a conversation between the guard and his family (who want him to retire) playing over it.
Played with in Archer. Lana mows down tons of mooks on purpose, but berates Cyril whenever he accidentally kills a mook who happens to be important to the mission at hand. In the third season finale, Archer also berates Cyril after one of his Leeroy Jenkins moments results in the death of a black astronaut - "That's like killing a unicorn!"
In The Avengers: Earth's Mightiest Heroes The Avengers are about to send Kang, his ship, and crew back to their own time (which will destroy them since their timeline no longer exists) but stop when Wasp tells them it will make Princess Ravona (who none of them have met) die. Never mind that they already sent hundreds of smaller ships back, and we saw that each ship was manned by one of Kang's men.
The Star Wars episodes of Robot Chicken gives us scenes of Gary the Stormtrooper, a nice guy and a family man who, though he enjoys some of the perks of it, is just working a job. Emperor Palpatine gets annoyed that the character focus is distracting from the story leading up to his very important death.