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.
Buffy the Vampire Slayer: In Season 5, Buffy kills several members of the Knights of Byzantium in the process of protecting her sister. But she can't bring herself to kill Glory, the hellgod who wants to sacrifice her sister, and eventually Giles has to do it for her.
Not... quite. It wasn't that she couldn't kill Glory, it's that she couldn't kill Ben, whose body Glory was using and who Buffy would have to kill as well. Buffy wouldn't kill an innocent person, even if it meant leaving an immensely dangerous enemy alive... but Giles would.
"She's a hero, you see. She's not like us."
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.
Doctor Who: This show is almost bipolar with this trope (along with What Measure Is a Non-Human?), not helped at all by the Doctor's personality varying wildly Depending on the Writer or the actor. 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 these days, since The Master is literally the only other surviving member of his race...
Also Foe Yay. They did used to be friends, after all, and both the Doctor and the Master appear to remember those days fondly.
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 Bad Ass... yeah.
Merlin: Subverted Trope 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.
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 Trope 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 a Guy of Gisbourne leading group of homicidal Flemish mercenaries. Will Scarlet wants to kill them but Robin says that that would make them no better than the Guy of Gisbourne. 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 a Justified Trope. 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 Trope. 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 on-screen 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 and does little more than knock her out.