After Voldemort's Death Eaters take over the Ministry of Magic in Harry Potter and the Deathly Hallows, the normal Ministry workers become this. They publish anti-Muggle propaganda and persecute Muggle-born wizards, even if they don't believe in it themselves.
Damon "Demon" Larkham in Matthew Reilly's Scarecrow. He runs a ruthless, highly efficient (they exterminate the Taliban) and technologically advanced band of mercenaries (called IG-88), but he still gets beaten by the heroes. At the end of the novel, he and his men corner Aloysius Knight. Just as Knight has a huge Oh Crap moment, Larkham gives a short speech about how "what happens on the field stays on the field," congratulates Knight, then walks away.
Most Lannisters who are not in the main line of succession are more affable and sympathetic than the descendants of Tywin Lannister. They basically carry their tasks out of duty to their household.
There are a great number of Freys that are not particularly proud in their role at the Red Wedding, but still carry out their household duties.
The Hound Sandor Clegane is an example of an innocent and rather kind-hearted individual that was moldered as a villain out of continuous sheer abuse. He might have gotten some redemption by shunning his Hound persona and (purportedly) becoming a grave-digger.
As seen in the quote above, the torturers of the Omnian Quisition in the Discworld novel Small Gods.
Also the original incarnation of the Cable Street Particulars. In Night Watch, they're a branch of the police accountable to no one where the stories about what goes on behind those doors are usually pretty accurate. Eventually, Vimes (alias John Keel) barges into their headquarters and demands of a man "WHAT DOES DADDY DO AT WORK ALL DAY, MISTER?" In spite of the man's protests that he's only a clerk, Vimes is still inclined to hold him accountable for the horrors perpetrated.
In Making Money, the villain has a "cleaner" on payroll for him who spends the book killing everyone who unknowingly assisted his boss in his scheme to become Lord Vetinari. When not killing, the assassin seems a normal enough guy and has an interest in reading for pleasure. The villain's other employee finds this more worrying; if the guy was The Brute, he'd at least be understandable.
Not quite a villain but Professor John Hicks - er, Hix, Head of the Department of necro- er, Post-Mortem Communications, is required by University Statute to commit moderately evil acts. These include pressuring people to attend community theatre productions.
Both the Thieves Guilds and Assassin's Guild are made up of punch clock villains; the former exists because Vetinari believes that if there's to be crime, it should be organized, sees off-hours thievery as one of the greatest offences against the guild rules, and makes a habit of helping beggars and taking in orphans. The latter provides the best education and tailoring on the disc, and its members are perfectly average aristocrats and the like who just, every once in a while, get paid to kill someone. Just business, I'm sure you understand.
In Kafka on the Shore, The character reads about Adolf Eichmann's trial. The man calmly planned the logistics for the holocaust, but thought of himself as just a clerk doing his job.
In the Doctor Who novel "The Resurrection Casket", the hideous interdimensional monster Kevin is not evil or ravenous, or anything a monster is. He'd be entirely content simply hanging out at a pub and watching a football game with his pals, but when someone is given a cursed piece of paper, he's duty-bound to kill them, or he'll be sent to a hell dimension until called back.
In The Dark Tower (the final book of Stephen King's The Dark Tower series) it's revealed that many of the Big Bad Crimson King's Minions were in actuality Punch Clock Villains, with the most prominent example being the decent, devoutly religious warden of the prison community where the "Breakers" — psychics who work to "break" the beams that hold all existence together — are held. He fully expects to go to Heaven once the job of destroying the Multiverse is complete, and to be well-received there.
He also makes sure the Breakers are treated very well (because they do better work if they're happy, but still). They get everything they want except the right to leave the grounds, and he has the man who raped one of them publicly executed.
Captain Ramballe of the French army that invades Russia in War and Peace is very much this. He sits down with Pierre in occupied Moscow and offers him dinner and wine, discussing how the Russians performed splendidly at the Battle of Borodino, commending them for such a fine job at defending their own country.
In If This Goes On a science fiction novella by Robert A. Heinlein, our hero is captured by the evil government. He notices that the several torturers for the government show no pleasure in their job, they are strictly business. It is implied that anyone who likes to inflict pain is not permitted in that job, as they are supposed to get information, not necessarily hurt people (although that is always an option if they think it will help).
Sergeant Zim and the other Boot Camp NCOs from the book Starship Troopers. While not technically evil, their job is to make sure that the 90% who can't cope with being in the M.I. or don't want the franchise bad enough drop out as early as possible. It is stated that the suffering they induce is too impersonal to be the work of a bully, that "Basic training is made AS HARD AS POSSIBLE, and for good reasons", and that all NCOs are decent (by NCO standards) to the ones who are left, when they know they are going to hack it. It's even pointed out that bullies tend to make bad instructors, since people who dole out misery for their own pleasure might get bored of it and start goofing off.
In accordance with the Truth in Television mentioned below, the British heroes of the Aubrey-Maturin series and their French opponents often enjoy each other's company when on land or after one of them has surrendered. One reoccurring Punch-Clock Villain is Captain Christy-Palliere, who eventually becomes their ally in The Hundred Days when the French military forces split between Bonaparte and Louis XVIII.
Good Omens features the Chattering Order of Saint Beryl, a group of Satanic nuns who are fairly ordinary people aside from helping to bring about Armageddon (via swapping the Antichrist for the baby of another family), and who regard Ax-Crazy animal-sacrificing Satanists in the same way that most moderate Christians regard certain "fire and brimstone" extremist Christians.
This is played for ironic laughs at the moment when the nuns do the switch, when the text informs us that it's possible that the nuns, as part of some dark satanic ritual, did something so terrifyingly horrible and evil to the baby who was swapped for the Antichrist that we would be horrified to our souls to hear of it; however, we can imagine that they made sure that the baby was given to a lovely family who would raise him well if we want to make ourselves feel better. It was later revealed to be the second option all along. Well, what did you expect?
Aziraphale and Crowley, an actual angel and demon respectively, consider fundamentalists and Satanists as a Vietnam veteran would consider a civilian who walks around wearing camo. Crowley himself has a job that involves tempting mortals into sin and bringing about Armageddon, but when he isn't working, he just likes to feed ducks in the park. Similarly with the nuns, he has a throwaway thought about Satanists who weren't crazy murderers, but did their rituals and went on being otherwise normal people. Then there's the fact that he didn't fall so much as saunter vaguely downwards.
Derk from Dark Lord of Derkholm is this trope in the extreme. He's a completely sweet and loveable wizard whose only wish is to work on his experimental creatures, but due to the extremely oppressive "boss" of his entire world, he's forced to play the Big Bad in his world for "tourists."
American Gods contains a disturbing example in the form of a glance inside the head of a kindly Nazi working the gas chambers in a concentration camp: "... and if there is anything he feels bad about, it is that he still allows the gassing of vermin to affect him. Were he a truly good man, he knows, he would feel nothing but joy as the earth is cleansed of its pests."
The antagonists of the novel (the modern Anthropomorphic Personifications like Media and the Technical Boy) also turn out to be this in the scene at the hotel. It turns out that they aren't evil, or at least not any more so than the old gods. The whole conflict is a set-up by Wednesday and Loki.
Czernobog is almost a literal example. Every winter he becomes dark, bad-tempered, and fond of caving in heads with hammers, and is the incarnation of a rather nasty god—although not evil in the strictest of senses, being still relatively friendly to the heroes. When springtime comes he transforms into his much nicer brother Bielebog.
Every baddie in The Grapes of Wrath, as lampshaded in a tragicomic scene where a fellow who's been forced off his farm tries to figure out who to shoot in revenge.
Some of the Star Wars Expanded Universe novels which focus on people working for the Empire embrace this trope. Allegiance has five stormtroopers whose consciences eventually override their willingness to take orders, though admittedly they didn't have a choice about leaving. Death Star is about a collection of people working on, well, the Death Star. A trooper, a gunnery officer, a cantina operator, a couple of convicts, a surgeon, a pilot, a librarian. It's also about Admiral Motti, Grand Moff Tarkin, and Darth Vader, so it's partly a Villain Protagonist novel, but the other characters all assumed the Death Star would never be used on an inhabited world. As the surgeon tells Leia while he's treating her after torture, he can't leave.
The gunnery officer who hit the final button to fire the superlaser was one of the main characters. He is immensely humanized; we learn that what he'd always wanted was to fire the biggest gun, that he sort of cheated in arm wrestling because a tendon had been torn and reattached in a stronger place, that he backed up his fellow gunners. He also followed orders. The prison planet, well, it was inhabited almost entirely by convicts, but some of them had been political prisoners or wrongfully convicted or guards. He saw Alderaan, though, as his personal Moral Event Horizon, making him one of the biggest mass-murderers ever, bringing him misery beyond his wildest dreams. He was the one saying "Stand by" when the Death Star was in range of Yavin - he knew that if he refused they would just get another gunner and give him a death mark, but he desperately didn't want to fire again and was fervently hoping that something would come up. And it did. Poor bastard.
As did Randall and a passing customer in Clerks, considering the deaths of civilian contractors on the half-built second Death Star. Although it's played with, as the passing customer — with reference to a friend of his who took up a contract on a house owned by a high-profile mobster that the customer himself warily passed on and got gunned down in a drive-by shooting as a result — notes that on some level even the contractors and non-military staff had to be aware of what they were getting into, even if they chose not to acknowledge it; it is essentially a massive death ray for a fascist empire in the middle of a civil war that they're building and operating, after all.
Also, from the New Jedi Order books is Yuuzhan Vong Shaper Nen Yim. While most of her colleagues are straight Mad Scientists, Nen Yim is legitimately trying to produce useful research that will help save her species from extinction, and she bears the victims of her experiments no malice or real ill-will. She ends up doing a Heel-Face Turn after realizing that her people have gone very wrong in the distant past and will rush headlong to their own self-destruction if they keep going like they have been.
All the others keep telling the non- Mad Scientist s that they have a god-provided Great Big Book of Everything which includes every design they could possibly ever need and the means to repair anything. Turns out that their current tech level is as far as the book goes, and there's no workable tech to repair what is already dying. when she finally finds this out she very nearly gets a permanent home on the funny farm.
In general a major theme of the SWEU is that there are a lot more Imperials who believe more in the Empire's Lawful side than its Evil side than vice versa. These types tend to be more amenable to Enemy Mines or Heel Face Turns; one of them, Gilad Pellaeon, even helped bring the Galactic Civil War to an end.
The demons, or spirits as they like to be called, are portrayed this way in The Bartimaeus Trilogy. At least until the third book.
This is a huge part of the premise to Salman Rushdie's Haroun and the Sea Of Stories. Big Bad Katham-Shud's henchmen are all unimpressive clerks who are doing very boring-looking jobs that just happen to be ruining imagination as we know it. Inverted by Katham-Shud himself, who looks like a Punch Clock Villain but is more of a Card-Carrying Villain.
In To Kill a Mockingbird, Scout-as-narrator explains that children of lawyers often assume that whatever colleague their parent goes up against in court is a bad guy, only to be mystified by the sight of them acting like friends when court's not in session. By the time of Tom Robinson's trial, Scout and Jem have outgrown this, and they're familiar enough with the prosecutor, Mr. Gilmer, to recognize and appreciate the tricks he employs, all in the spirit of a fair trial. Neither of them is quite old enough to realize until the guilty verdict that that's not what's going on this time, and for the case of a black man accused of raping a white woman, no one's bothered hitting any punch clock.
The whole point of the book is Scout's opportunity to see her perfectly normal neighbors condemning a good, innocent man. There is no punch clock because the jury is following ingrained social custom, the same as they do every day.
The summoner-for-hire Binder from The Dresden Files book Turn Coat mostly just wants the bounty on Morgan. He doesn't have anything against Harry personally, it's just that he happens to be on the other side of the issue. Harry lets him get away for this (and other) reason(s).
Subverted by some of the other creatures Harry encounters. They try to play this card with varying success over the course of the series.
While some of the Black Ajah in The Wheel of Time are genuinely evil, many joined it only for the opportunities of power it gave, and are not particularly keen on that whole world-destroying stuff.
In Jack Vance's Planet of Adventure, the hero is once approached by a well-dressed man who introduces himself, informs him that the Assassin's Guild has taken out a contract on him, and asks him to roll up his sleeve. Hilarity Ensues.
In Bernhard Schlink's The Reader, a former concentration camp guard is on trial as a war criminal, mainly because she was given the task of making sure that none of her prisoners escaped during a march. On an overnight stop, the prisoners were locked in a church, which caught on fire. Rather than risking disobeying orders by showing the prisoners mercy, the guards chose to leave them locked inside while the building burned to the ground. When confronted about it, she seemed confused that she was on trial despite having followed her orders, and asked the judge, "What would you have done?" This from a woman who had at other times shown kindness to the prisoners.
In several place, The Bible mentions tax collectors as among the most disliked members of society. Back then they were considered little more than thieves employed by the government. The Roman Empire often made use of "Tax Farming," the practice of selling the authority to gather tax moneys. The purchaser could squeeze people as hard as they liked under the tax laws, and any extra they got was profit. This practice was common in Europe through the Middle Ages, and is likely the cause of the heavy taxes often mentioned in Robin Hood and similar stories. That makes this trope is Older Than Feudalism.
In Theodore Cogswell's short story Wolfie, Dr. Arsoldi is a sorcerer (in denial as to his accomplice's demonic nature) in New York City specializing in helping murderers commit the perfect crime. He also has to stand security; if the murder falls through, it's off to Hell he goes. At the time the story starts, he's already had one close call. Naturally, the next job is a textbook case of Epic Fail.
In The Two Towers, Faramir remarks about a fallen foe (a member of an army marching in support of the Dark Lord), "His sense of duty was no less than yours, I deem. You wonder what his name is, where he comes from, and if he really was evil at heart. What lies or threats led him on this long march from home, and would he not rather have stayed there... in peace?" (This rumination was cut from the theater version because it was such a long movie.)
In Death: Sylvester Yost from Betrayal In Death is very much this. He kills people because he's paid to, and he looks at what he does as a job in which he puts a number of years into it, and then he can retire and live in what he considers relative peace. Don't believe for a minute that he's a great guy, however. On the job, he rapes his target and strangles him or her with silver wire. He is The Sociopath and needs to be stopped.
Tales of Kolmar has the villain hire mercenaries to go after someone. She is defended by an ex-mercenary who sees through their attempts to get casually close and warns them that they can leave now and it'll be fine, but if they go after her they're all dead, and urges the youngest one to leave the profession. The mercenaries do go after their target and are repelled, losing several of their own. After that, shaken, the youngest one decides that he's had enough and quits, and all the older mercs are pleased for him, but they won't quit a contract. All of them get killed.
Prisoners of Power aka Inhabited Island briefly explores the chilling effect of this trope being played seriously. A captured insurgent sneeringly tells his interrogators that their hate and passion makes them ineffective at cracking him, because it's just too easy for him to see them as enemies who must be defied. Now when he had been tortured by some small-time drones who didn't give a shit about him or the reasons he'd been tortured for and showed more passion at filling the accompaning paperwork or cursing their wretched pay than at sawing off his arm, then he'd been terrified to the bone.
Lawrence Block's Keller is just a normal guy who likes dogs and stamp collecting and just happens to be a Professional Killer.
A lot of side characters in Richard Stark's Parker novels (though not Parker himself) are just people happen to making a living through thievery. Most notable is Alan Grofield who thinks of himself as an actor, not a thief. Robbery is just what he does to keep his summer stock theater company afloat.
In Apollo's Grove, a mercenary band attacks the temple of Apollo at Delphi in order to kidnap the Oracle. The captain of the band kills a temple priest without a second thought and threatens to massacre the entire temple group. But he does so with no hostility, explaining that everything he's doing is a business decision. He also urges the priests to bury their dead colleague, as he died with courage and conviction.
Lampshaded in Ivanhoe. It is noted that the Templar guards will execute Rebecca in a heartbeat but will not allow Bois-Guillbert to sexually harrass her before her sentence.
Adventure Hunters: Zambwe is hired to capture the adventurers. He has no grudge against them nor any stake in the Evil Plan. Once he has been paid for this job he disappears from the narrative.
Ben's stepbrother is this in the children's novel Skymaze, as the Matrix-esque game makes him a villain and forces him to try to kill Ben every time they play.
Probably most of the Capitol citizens who work for The Hunger Games as stylists, beauticians, escorts, etc. They may be involved in the politically oppressive annual murders of teenagers, but they didn't establish them, they don't rule Panem, and in the grand scheme of things, are basically just government employees. There's also the fact the government expects obedience out of everyone: them included.
Andrei Belyanin's On-call Demon has the protagonist Abifasdon working as a collector for those who have sold their soul. His wife is working in Hell's Temptation Department, seducing humans and getting them to sell their souls for pleasure. Abifasdon's best (and only) friend is a SWAT-type angel who beats up Abifasdon every day. The main plot of the novel? Abifasdon and his wife trying to have a baby.
In Please Don't Tell My Parents I'm A Supervillain, Penny's parents imply that most supers on both sides are just in it for the brawl, rather than an actual desire to do good or evil. Lucyfar, especially, is noted to switch between hero and villain on the fly.
Gand Ioratth in Voices, the second in the Annals Of The Western Shore trilogy. He's the leader of the occupying Ald army in Ansul, which is incredibly oppressive (books destroyed, religious freedom crushed, women raped and old men beaten, etc), so naturally most of the population hates him and the local Rebel Leader wants him dead. The first time Ioratth appears in the flesh, though, he's being impeccably courteous to Orrec (the previous book's hero), shows vocal disdain for his rude, zealot son, and we're told that he treats his Ansul lover well. Ioratth is actually quite pleased when he gets orders telling him to be less oppressive because he considers the whole venture to be a waste of time; he's only doing it because he's an Old Soldier following orders.