However, the reason Dech dislikes killing major villains isn't morality, it's pragmatism. He gets paid for thwarting villains. If he takes them in alive, they can potentially escape from the Cardboard Prison, at which point he can get paid for thwarting them again.
Girl Genius: Both on the official cast page and on this very wiki, Zola's Minions are called "A bunch of guys in funny hats who appear to be along to carry the equipment and get killed". Although in this case, the Cannon Fodder is fed to the sadistic and insane trap-filled castle, rather than the hero(in)es.
Master Payne points out that even when dealing with faceless mindlessly aggressive monsters there can be ugly problems.
Subverted and inverted in Terinu, as the main cast shoot down attacking Galapados warriors with no remorse, even blasting a breeding facility without a qualm to cover their escape. An act that is immediately inverted when the Galapados leader contradicts the Big Bad's orders to go after them, in order to save the dying Galapados clones.
Lampshaded very effectively in thisTom the Dancing Bug.
ARG! My hopes and dreams!
Parodied in thisPenny Arcade strip. A mook is not so happy with his boss' escapades and is thinking about switching sides and—oops.
In one of the World of Warcraft based Dark Legacy webcomics strip, a gnome is killing kobolds and gathering their ears for a quest. Upon killing a kobold, the gnome checks the kobold's wallet, and sees a picture of his wife and kid. The gnome seems heartwrenched to learn that he just killed a family man... but then he kills the wife and the kid for their ears.
In Sonichu, especially during the final two issues, the characters are more than happy to mow down hundreds of Jerkops and Decepticlones. However, during the ninth issue, it's revealed that the Jerkops were actually brainwashed people. But, for Chris, Sonichu and the like, that's okay, because they were in his way of Chris' great Love Quest.
Mushroom Go shows the measure of a mook in a flashback. Too bad the mook in question is Captain Martello's father.
Discussed (but not in the sense of Discussed Trope) in Sluggy Freelance, chapter "Aylee", when Torg and Aylee are hiding in an alternative dimension where Earth has been overrun by mysterious, fairly mindless-seeming "ghouls". They spend some time killing them practically for fun in creative ways, until Aylee starts feeling bad about it and mentions it to Torg, who says he just felt like taking a break from previous moral ambiguity by messing with straight-up bad guys, but they should probably stop. It all causes additional guilt later when it's finally revealed just what the ghouls are.
Touched on in Guidestuck when Jaspers prototypes Bec's pet dog, forcing the imps to take on the appearance of his dog Jade.
A Fairytale for the Demon Lord: Plays with and Deconstructs it. The Knights are all nameless, sometimes unthinking, cannon fodder, and if they perform heroic deeds, they get an name and identity. The main character is a knight who rejected the mindset and a name after saving the princess. As time goes on, he shows no remorse killing knights who get in his way, or are even witnesses. In one of the backup stories, a random soldier is seen digging up the remains of dozens of nameless knights under his command to bury them properly, with blank tombstones reflecting their nature. It's really Balder who seeks to go out and kill the protagonist, and give them names on their tombstones written in his blood to honor them.