In ElfQuest: The Searcher and the Sword, Shuna (who's been living with the elves for about two years) goes and gets married to a human man, who starts off with just bad vibes but quickly jumps off the slippery slope and becomes a full-fledged wife-beater. After he beats her the first (and only) time, she fights off typical "maybe my love could change him" reasoning, beans him one last time, and flees. Her erstwhile husband and three or four human fighters pursue her. For the showdown? One of the Mooks makes ready to shoot the elves point-blank while they're in a hole; Strongbow responds in kind. That's one down, deader than dead. The elves quickly subdue the rest, Shuna duels her hubby, and then they tell them to leave and never come back.
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.
Parson from Erfworld has little Heroic B.S.O.D. when he realises that he killed around a small nation worth of soldiers. While others think "they were just units" Parson considers them real people.
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.
Goblins is actually an attempt to explore the other side of this trope... by starting off in a goblin battle camp, with a handful of goblins, guarding a chest, and what happens when an adventuring party stumbles upon them. The surviving goblins become adventurers, and attempt to change their lives... making the 'adventuring parties' and the nearby towns into mooks.
Well, not quite. The heroes still try to avoid killing anyone other than the (justifiably) Always Chaotic Evil Elite Guards.
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.
The Adventures of Dr. McNinja: Plays with it, and plays it for laughs. The Doc has no trouble killing guards and mooks. In one comic, there's a guard happily strolling around thinking of his family, when he gets his neck snapped, and the Doctor misunderstands what he was talking about it.
When the Doc kills a bunch of Ninja mooks, the mother of one of them calls him out on it... at the funeral for The Doc's mentor who the ninja mooks had ruthlessly gunned down. Despite this he still has nightmares about killing all those people.
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.