Angel: In Season 5, Gunn, losing his legal upgrade, makes a deal with Dr. Sparrow to permanently improve it in exchange for improving it, by signing a Customs release form to get something out of it. That something turns out to be Illyria's sarcophagus, and her essence escapes and infects Fred, killing her and turning her body into Illyria's avatar. In the next episode, when he's found out by Wesley, Gunn confesses that he was fully prepared for something terrible to happen in exchange for Sparrow fixing the upgrade... as long as it wasn't to anyone he knew.
Gunn: I didn't think it'd be one of us. I didn't think it'd be Fred.
In Agents of S.H.I.E.L.D. no one raised any objections to a handful of guards just doing their jobs getting killed to get a drug they needed to save one of their own team members. Which is especially jarring when Coulson is horrified enough just at the suggestion of killing Victoria Hand that it makes him realize Agent Garret is the evil mastermind.
In this particular case, the guards were actually working for the good guys. Since Hydra had no knowledge of where the T.A.H.I.T.I. project was, those guards must have been loyal to Fury.
Oliver Queen in Arrow always gives his high-profile targets a chance to "do the right thing" before announcing that they have "failed this city" and planting an arrow in their hearts. He extends no such niceties to their hired goons, dropping half a dozen in a typical episode (many more on occasion) with seemingly little regard for whether they live or die from their grievous arrow wounds. This becomes a plot point in the Huntress-based episodes, where he tries and fails to communicate this to Helena (and it doesn't help that Helena has a deep vendetta against the mob). He eventually admits that killing mooks wasn't much better than killing indiscriminately.
Also Played With. In the earlier seasons (where Oliver was very willing to kill) he usually needed the high-profile criminals alive so they could reverse the damage they'd done. In later seasons, it appears that Oliver kills mooks left, right, and center while still adopting Thou Shalt Not Kill towards named characters, but closer analysis reveals that he usually uses sedative-syringe arrows.
Horrifically shown in Season 5 episode 9, Prometheus has recreated one of "The Hood's" kills from a flashback set early in Season 1, every single dead mook is replaced with another person, freshly killed in the same manner, the only one not dead at the new scene is the boss, who has been replaced by a very much alive Prometheus.
The Avengers: Steed and Mrs. Peel typically kill half a dozen or more mooks and henchmen without breaking a sweat (or a nail). They're quite indiscriminate, though: the Big Bad usually gets killed just as unceremoniously.
Diaz: Hey, thanks for shooting that guy. Boyle:(chuckles) Hey, my pleasure. Perp: Your pleasure? This was a human being you just killed. Bill Perp had a family! [after a beat, both Boyle and Diaz decide to shoot the Perp again]
Burn Notice: Averted Trope: In his earlier missions (before the beginning of the series), Michael played this trope straight. Realizing he was becoming less the man he wanted to be, he began to change the way he approached his missions. Though still willing and able to kill when strictly necessary, both Michael and Sam want to keep the body count as low as possible; Sam is especially adamant, particularly in the final season, wherein, by Michael's explicit admission, he serves as Michael's primary moral anchor in the face of the growing moral ambiguity which defines his current assignment. Jesse and Fiona are somewhat less insistent, but also desire to keep deaths to a minimum. Other, more minor characters, such as Michael's various CIA handlers and peers, serve as counterpoints and foils to the main characters, playing the trope more or less straight.
The most obvious example is his repeated attempts to save the Master, despite easily (if reluctantly) killing anywhere from several dozen to several million nameless enemies in numerous other episodes. Somewhat better justified in the Tenth Doctor stories, since he and the Master thought that they were literally the only surviving members of their race... Also there's a lot of Foe Romance Subtext. They did used to be friends or more, after all, and both the Doctor and the Master appear to remember those days fondly.
As part of her journey to becoming the Doctor's Distaff Counterpart, Clara Oswald in "The Magician's Apprentice" not only overlooks the fact Missy (aka the Master after a Gender Bender) has just killed a number of UNIT personnel, she immediately agrees to team up with her in order to locate the Doctor.
Another controversial and glaring example is "Resurrection of the Daleks", where the Fifth Doctor kills several Daleks personally throughout the story and unleashes a biological weapon on them at the end, but can't bring himself to shoot Davros when he has the chance.
Heroes: Pointed out when Danko is talking with Nathan about how his plans have been ruined thanks to Nathan's interference. Nathan retorts that people could have died, and Danko counters that people had died, if one considered Danko's Mooks to be people.
And then Danko causes heads to bang walls everywhere when he inexplicably feeds one of his men to Sylar to allow the latter to use the man's identity as cover.
Lily: So when they blew up the Death Star, those were people on that thing?
Human Target: The main character, Christopher Chance, seems to have no problem mowing down security guards in one episode where he breaks into a large corporation. Although the company was selling weapons to terrorist organizations, such dealings would probably be beyond the knowledge of normal security personnel.
This actually happens throughout the series. Christopher Chance regularly mows down Mooks, and kills the Head Mook. The episodes actual Big Bad however, is usually arrested.
Knight Rider: Occurred at least once where a young child was playing with a beach ball in the garden of the kidnapper, and the mook in question was entertaining her. There was no real communication - just a few minutes of play and him passing the ball back to her, but given that this guy had been quite ready to seriously hurt someone in the other room and was portrayed as a bit of a silent badass... yeah.
Legends of Tomorrow makes a big deal out of how small changes to the timeline can have big consequences to the present day and future. Except when it comes to villains and their mooks, who the team kill with impunity on a regular basis.
Merlin (2008): Subverted in the series 4 finale. Merlin kills the five guards but leaves Agravaine alive for some reason. And then they talk, and it quickly becomes clear (although not to Agravaine) that Merlin intends to kill him too, and that his survival was just a fluke. Okay, he waits until Agravaine pulls a knife to actually do it, but he also waited for the Faceless Goons to rush him.
Throughout the first two seasons of Once Upon a Time, it's made clear that killing the Queen isn't the answer, and in fact if Snow White were to kill her, she'd become just as evil. Never mind that it would be the smart thing to do, to stop Regina's Roaring Rampage of Revenge. Snow White and Charming regularly kill guards on-screen, however, and when Red Riding Hood in her wolf form massacres several dozen soldiers, it's treated as fodder for jokes.
Addressed during episode 3. To him, the guy who Danny killed was just the Militia member who killed his dad. To a fellow Militia soldier, he was a friend, with a loving family, and a name: Templeton.
And then completely ignored as Charlie and company slaughter entire squads of militiamen at a time.
The rebel side comes in for this as several people are introduced for one whole episode, and then are all slaughtered by Wheatley.
Robin Hood: Mostly averted in the BBC series, where Robin, tired of war, deliberately avoids killing anyone, including Mooks (and the Sheriff is Genre Savvy enough to notice, so he doesn't take Robin's threats seriously). He breaks the rule several times, such as when he slaughters dozens of the Sheriff's men when he thinks that Marian is dead, or killing a few Arab assassins trying to kill King Richard.
Robin of Sherwood: Lampshaded where there is an argument between Robin and Will Scarlet after they have captured Guy of Gisburne leading a group of homicidal Flemish mercenaries. Will Scarlet wants to kill them but Robin says that that would make them no better than Guy. Will replies 'Well what makes you think we are any better? What about all the men-at-arms we've killed?'
Rome: Played straight, lampshaded, and then becomes justified. When Pompey flees to Egypt, he is captured and executed by a soldier loyal to Caesar. Caesar, who has no qualms killing Pompey's men, is livid that a nobleman would be killed by a commoner and ultimately executes the soldier and desecrates his body.
Historically this was generally what happened, although Caesar's reasons for anger were less about who killed him, but that his usual process was to spare his military rivals and thereby gain popularity for his mercy. He was not a man driven by revenge but by what would get him the most control over a situation and cause the least disruption to the safe progress of his burgeoning empire (nee republic). The execution of Pompey gained him nothing militarily or politically, and he took out his disapproval on the over-zealous Egyptian authorities afterwards.
Plus, it served Caesar's interests. He wanted to overthrow Egypt's leadership. What better excuse than righteous indignation about how terribly a Roman consul was treated? His enemy Pompey is eliminated, he gets credit for having intended to pardon him, and a dangerous province's leaders are replaced with a new set loyal to Caesar. Perfect.
The Vampire Diaries: Caroline sees no problem in trading a hybrid's life for Elena's, even though he had broken Klaus' sire-bond and only wanted to get away from Klaus.
Walker, Texas Ranger: The title character will slaughter any mostly harmless Mook on the way to the horrifyingly evil Big Bad, but when he gets there, he usually spares the villain and preaches a Broken Aesop.
The Wire: Inverted. Several mooks die throughout the series as the cops try to take down the gang lords. Most of them get a great deal of characterization and their deaths visibly haunt the cops throughout.
Wonder Woman (2011 pilot): Critics of the failed 2011 pilot have called out the lead character for this. After beating up (and by onscreen evidence killing in a couple of cases) several Super Powered Mooks, Wonder Woman proceeds to successfully deflect a standard human guard's bullets easily before throwing a pipe through his neck, killing him. Moments later, she encounters the Big Bad (who actually takes a moment to pay tribute to the newly deceased guard) and does little more than knock her out.
The Wrong Mans: This trope is actually subverted in the climax of the second series, when one third of the Big Bad Ensemble is actually the brother of a nameless mook terminated by Paul Smoke in the previous series, out to both tie up loose ends from the previous series and seek revenge. When he finds the person he thinks is responsible, he angrily holds them at gunpoint and asks why he did what he "did".
Brilliantly averted in Six Feet Under. Even though the deaths that open every episode usually happen to characters who are never seen before or after, they're all given personalities and backstories, which usually become crucial plot points in the corresponding episode.