Colonel Cutter from Antz is the more serious and competent kind of Punch Clock Villain. When sent to fetch Princess Bala, the first thing he does to get some attention is punch a hippie bug in the face. But when it comes to committing genocide, he feels that's taking it a little too far.
In Wreck-It Ralph, the titular character is this in the 8-bit game Fix-It Felix, as well as most of the other video game villains in the arcade where the film takes place. The only exceptions are the Cy-Bugs from Hero's Duty, who aren't Animated Actors like the other characters due to flawed AI programming.
Done in Monsters, Inc., where the monsters' sole purpose for scaring children is to use their screams to power their world.
Sully:(to Boo) Look, I'm not gonna scare you. I'm off duty.
Films — Live-Action
In Clerks, Dante and Randal debate the ethics of the Rebels blowing up the Death Star in Return of the Jedi, given that many of the workers building it were probably independent contractors with no particular allegiance to the Empire.
The current customer overhears and just happens to be a contractor himself. He shares a story about how he turned down a job for a mafia boss despite the lucrative paycheck. His buddy took the job instead and ended up getting hit by a stray bullet and dying during a drive-by attack on the mobster's house. The moral being that even a punch-clock villain has to accept the risks and moral cost of the job, and anyone who took a job on the Death Star has themselves to blame.
Vincent and Jules from Pulp Fiction relate to this trope. One minute they're chatting jovially about mayonnaise on fries. The next, they're pulling off the hits they're paid for. It's subtly lampshaded in an early scene: arriving at an apartment for a hit, they check their watches, find out it's not time to go on the clock yet, and hang back a few minutes to finish a conversation they were having.
A couple of Regional Bonus scenes from the first Austin Powers film show Dr. Evil's security mooks to be family men with normal social lives, and explore the tragic results of their death. These scenes appeared in North America as DVD Bonus Content.
Although they don't get paid per se, this trope sums up the entire point of the killer robots in the Terminator franchise. They hold absolutely no bloodthirst against their intended targets. It really just is a job to them, and it can't be anything else. Consider the classic scene from the second movie when the "hero" T-800 is about to kill some dumb jocks who were just screwing with John...
John: You were going to kill them!! The Terminator: Of course. I'm a Terminator.
In the film Bon Cop, Bad Cop, Officer David Bouchard recounts killing a houseful of criminals, but sparing the vicious attack dog because it was "just doing its job."
This is the point of Terry Gilliam's Brazil, where the primary villain isn't so much individual cruelty (although there's plenty of that going around) as the collective effect of simple apathy from a society of bureaucratic jobsworths. Jack (Michael Palin's character) is an extremely good example.
In Blade, as the eponymous hero is killing the Faceless Mooks, one of them tries to save his life by saying "No... please! I just work for them!" If "they" hadn't killed the hero's mentor, it might have worked.
The hired thug going after Max and Agent 99 is actually dealing with marital problems. Max, having stated early in the movie that evil is what villains do, not who they are, uses this information to save both himself and 99, and inspire this villain to become the Reverse Mole for him later on.
After putting up with yet more verbal abuse, Shtarker at one point gripes that he wants to quit, but can't because Siegfried is married to his sister.
The Mortuary Keeper in MST3K'ed film Space Mutiny. He's just there running the facility where failed Mooks are frozen until necessary. He may work for the villain but when the heroes arrive he asks if they need help or would like a cup of tea. He also answers all their questions about the Big Bad's Evil Plan. He doesn't really seem evil at all.
The Godfather films, especially the first and third, have organized crime bosses say "it's not personal... it's strictly business" (or some variation thereof) regarding their business affairs. The one scene from the novel sadly not in the movie had Michael comment on this and call it rubbish. He then goes on to describe his father as never treating his affairs as "just business" and speculate this is what had made him great.
Although there are no direct examples, the film Cube implies the builders of the eponymous Death Course were of this nature.
"Who do you think the establishment is? It's just guys like me. Their desks are bigger, but their jobs aren't. They don't conspire, they buy boats."
Dee Jay in the Street Fighter movie, who not only does his job only for the money, but clearly hates every single person in the organization, as he also doubles as the Deadpan Snarker. He ends up trying to escape with Bison's money only to find out that it's Bison dollars, which are worthless.
The East India Trading Company marines in "Pirates of the Carribean: At World's End" can fall into this trope - they are not faceless mooks, but soldiers, and throughout the film, you can see groups of them get genuinely disturbed or upset by the ensuing weirdness that doesn't seem to affect their employer or other characters (particularly when they find a macabre 'breadcrumb' trail of marine bodies). They have, by far, the highest body count of any group of people in all four films to date.
The teen protagonist of The Manhattan Project is hunted by gun-toting government agents that repeatedly threaten to kill him if he does not turn over his homemade nuclear weapon. One of these agents assures him it was nothing personal later in the film just before they may all die in an unintended detonation. (And in all fairness, they were government agents acting legally to protect the public from an unauthorized Plutonium-Bomb!)
"And then I realized they were stronger than we. Because they could stand that these were not monsters. These were men... trained cadres. These men who fought with their hearts, who had families, who had children, who were filled with love... but they had the strength... the strength... to do that. If I had ten divisions of those men our troubles here would be over very quickly. You have to have men who are moral... and at the same time who are able to utilize their primordial instincts to kill without feeling..."
This is actually a distorted retelling of another sort of punch-clockery: soldiers in the Belgian Congo were accused of wasting ammunition, so they were told they'd have to bring back a hand for every native they claimed killed... so to save some ammunition for hunting, they took to cutting off hands from the living. John Milius took an example of barbarism for pecuniary gain and turned it into a parable of how thinking men can turn themselves into monsters for an ideology....
Repo! The Genetic Opera has the Genterns, sexy sadistic nurses who put up with an awful lot for their well-paying jobs (including occasionally being raped or murdered by a Largo child). There's also the Repo Men, sociopathic organ retrieval experts armed with very large scalpels. One of the Repo Men is a protagonist—he's shown as being a sweet, slightly campy, doting family man when not on the job.
A Take That is delivered in Taken, where Patrice, the auctioneer of the would-be sex slaves, tries to insist that "It's all business. It wasn't personal!" Since his last "sale" was Bryan's daughter, "It was all personal to me" and Patrice gets the rest of the bullets in Bryan's pistol clip.
Arthur Brooks, the social worker in Big Daddy, probably qualifies as this - until the climactic scene, where he (along with everyone else in the courtroom) gets a Pet the Dog moment when he pays a call to his father.
In The President's Analyst, an American and a Soviet agent are old pals who place a friendly wager on who'll catch their common target first, going so far as promising to leak info so the other guy would get stationed to where the loser would buy the winner dinner. Another agent puts off assassinating the title character because his bullets are inconveniently far away and he told the wife he wouldn't work late.
In The Island, the mercenary helps the heroes the moment the job is finished.
Inglourious Basterds uses this trope in full. While the Basterds view the German army as a bunch of Jew-killing monsters, the majority of Germans outside of Hitler and Goebbels are portrayed as decent, loyal soldiers. One German officer refuses to give information that would get his men killed, and gets beaten to death for it. In one of the most heartbreaking scenes, several Basterds infiltrate a bar where a group of soldiers are celebrating one's new baby boy. When their cover is blown, the shooting starts. Everyone but Bridget and the new father are killed in the ensuing gunfight. When the soldier begins to surrender to the Basterds upstairs, Bridget shoots him in the back to try and keep her cover.
Sharon Stone's character in the original Total Recall (1990). She said it best, "I just work here".
In District 9, Wikus (pre-Character Development) and most of the other non-military workers can be seen as these. The awful way they treat the prawns stems from nothing personal, but is simply how they've been instructed to do their jobs.
Shoah is a documentary about the Holocaust. Many of the people interviewed by the director were "just doing their job" or "following orders" when they participated in the organized extermination of Europe's Jews.
All the hitmen that go after Jason Bourne in The Bourne Series are just doing their job. When off the job, they hang out with their kids, meet up with executives of their company or just travel around the world. Certainly not played for laugh, considering how the series completely abstained from any comedic relief.
Captain Louis Renault in Casablanca, who makes it clear he's happy to cooperate with the Nazis as long as they remain in power, without caring about their ideology one way or another.
Inigo Montoya and Fezzik are punchclock villains while working as goons for Vizzini in The Princess Bride. Inigo even states outright, "I only work for Vizzini to pay the bills." Vizzini also reminds Gentle Giant Fezzik of his former status: "unemployed in Greenland."
The Mexican has a cute one: James Gandolfini playing Winston Baldry abducts Julia Roberts because "it's my job", then the two of them start a girly friend relationship (turns out this punch clock villain is also a Badass Gay) and just to prove this trope right he executes a Heel-Face Turn.
In The Cabin in the Woods, all the people working at the facility. An example of the darker side of this trope, as the fact that it's just a job means they set up a betting pool, pride themselves on good work, and have a party once it's over. They don't do it out of malice, but they don't care or regret it either.
Paul has the ineffective and affableMen in Black Haggard and O'Reilly, who're chasing the main characters because they were told to and have no idea that they're after an alien refugee. Deconstructed once they do find out, because they figure that they can get a promotion and start getting a lot more ruthless and determined, if not more effective. Especially Haggard, who goes from a friendly Nerd to shooting Ruth's father.
Jackson, who presides over the highest security wing of the prison in Felon is a violent, fouled mouthed and intimidating man inside the prison, but a highly personable family man outside. He fears for his life and decided that the only way to control the toughest criminals in the prison is to make them fear him by outplaying them at their own game.
A henchman in Iron Man 3 surrenders in the face of Tony's attack almost immediately:
Henchman: Honestly, I hate working here. They are so weird.
The Little Rascals 1933 short "Bedtime Worries" has Spanky encounter a burglar as he's in bed. He tries to warn his parents, but they don't believe him as he's been constantly calling out to them through the night. The burglar is actually nice enough to give Spanky a glass of water and then tuck him back into bed before robbing the house!
Star Wars has the Clone Troopers, who, on the orders of Chancellor Palpatine, turn against their Jedi commanders and slaughter them. Howeveer, they're not really evil per se, they're brainwashed war slaves only doing what they were literally programmed to do: follow orders without question. You can even hear how sad one of the clone pilots sounds when he's ordered to turn his fighter's guns on his Jedi squadron leader.