24: You have the Well Intentioned Extremists who often serve as the Big Bad. But most of the Mooks are simply punching the (villain) clock and are only out to collect a check. Most of them will Heel-Face Turn once they are caught or at least cooperate with the authorities since they never really bore anybody any ill will. But they're villains so they usually demand immunity or some other kind of deal.
Played with. When the title character meets a vicious-looking demonic prison guard he has to defeat. The demon reveals his name is Skip and he commutes to work. Skip is sympathetic to Angel's situation, but is obligated to fight Angel anyway; when he is defeated (Skip later claims he took a dive) Angel makes sure he's not badly hurt before knocking him unconscious. Although in this case, Angel himself fits the trope better. Skip is guarding a guy who is supposed to be in Hell and Angel is there to break him out because he has to in order to save Cordelia.
Skip later turns out to play a larger role in the show. First he helps Cordelia become part demon to cope with her visions. Later on, it was revealed that he did this because he was working for the goddess Jasmine, who kills Cordelia and tries to take over the world. This makes him less of a Punch Clock Villain and more of The Mole.
When the cast takes over Wolfram and Hart they find that a lot of the people there will just go with the flow. Work to bring about apocalypse, work to help people, whatever, what's my bonus package look like? Lorne reads everyone to screen out the truly nasty people, and they get along okay. That said, there were a few goofs. Eve and Sirk both turned out to be plotting with Lindsey to kill Angel. One of their doctors was part of an extreme gourmet food network, and had Nina kidnapped to be eaten alive. And Knox secretly worshipped Illyria, and decided that Fred would make a good host for it. There also had a demon who liked to dismember virgins for fun.
In season 4, John Sheridan was tortured for weeks on end by a banal inquisitor attempting to gain a signed confession out of him in exchange for his freedom. The inquisitor makes a big deal about never telling a lie, neglecting to mention the truths he conveniently omits, such as offering Sheridan half a sandwich in exchange for some small act of cooperation and not mentioning the fact that the poison within it will give him a night of horrible illness. Adding to the banality of the inquisitor's evil, near the end of the program, when the inquisitor has completely failed to get what he wants from Sheridan, he is simply replaced with another, who begins having the same conversation the first inquisitor began with.
Sebastian AKA Jack the Ripper from the episode "Comes the Inquisitor" may have tortured Delenn and Sheridan during his testing of the two, but once they passed the test that was the end of his hostility towards them.
Mr Endawi, of Earth Force Intelligence from the Third Season Primere who comes to Babylon 5 to snoop around about reports of the Shadows. What is interesting is that he apparently doesn't know he is being used to help cover up a Government Conspiracy to cooperate with the Shadows. The orders he is given are exactly the ones a Reasonable Authority Figure would have issued in the same circumstances. His superiors simply intend to use the intelligence for sinister purposes. But as far as Mr Endawi is aware he is just being a good officer following perfectly sensible orders; it is the actual purpose of the orders he is unaware of.
"Flesh does what it's told... or they become most annoyed."
The Technomage Trilogy and its prequel, ''The Shadow Within'' also indicate that Morden offered to serve the Shadows "to the best of his ability" in exchange for freeing his wife and daughter from being trapped forever consciously in a bubble of hyperspace after a tragic transport accident, and allowing them to die humanely—supposedly the Shadows were able to do that, whether or not they really did is something we never know.
Breaking Bad: "Mike" is a professional hitman, as well as a multitude of other jobs that generically make life easier for criminals. Although he confesses to enjoying his job, he is also shown to be somewhat of a clear-headed softie, and a caring family man.
Covert Affairs: Foreign Police. Sometimes even American police. Naturally they don't want Annie working in their country, at least not without them knowing what she is doing. But the police are doing their job as police and Annie is doing her job as a CIA agent.
Dark Angel: Though in most ways the opposite of this trope, Max goes in that direction in her pre-hero career. When confronted with the supposed immorality of her burglary, she replies indignantly: "I steal things in order to sell them for money. It's called commerce."
When the Ogrons appeared they are portrayed as a Servant Race for the Daleks. However IDW comics shows this was more a job and due to the Doctor defeating them they are in economic trouble. An Ogron diplomat even helps the Doctor and by the end the Doctor helps the Ogrons get work with the Shadow Proclamation.
The Thals and Kaleds in Genesis of the Daleks seem to be portrayed as this. The Thals are using brutal methods in their war against the Kaleds such as enslaving people and forcing them to do work that will kill them but once they think they have won the war they decide to free all their prisoners and some Thals even prove helpful to the Doctor when the Daleks attack them. The Kaled scientists are doing research that will lead to the creation of the Daleks but most of them are shown to be opposed to Davros ultimately.
In another instance, the Doctor gets some righteous fury on the workers of the Bad Wolf corporation; a television company with gameshows that end in murder. When one of the managers claims that they're just doing their job, he angrily tells her that she has now lost the right to even speak with him.
Most employees of the Torchwood Institute tend to be Punch Clock Villains; however, over in Torchwood, they're the main characters. They're usually different members, though, with Captain Jack explaining that he rebuilt and changed Torchwood after they got destroyed in the Cybermen invasion.
In Time Heist, bank security is incredibly polite about the fact that they're going to kill you, and really wish you wouldn't make such a fuss about it.
The Dukes of Hazzard: Tends to leave the audience feeling more than a little sympathetic to the deputies working under Sheriff Rosco and Boss Hogg. Most of the sympathy fell on Enos Strate, who was genuinely sympathetic and actually had a crush on Daisy Duke. While his replacement Cletus Hogg wasn't as much an Anti-Villain, he generally pointed out that it's nothing personal; he just wants to keep his job and not be a shame to the Hogg name.
Subverted Trope when Jubal Early claims to only hurt people because it's part of the job, River replies that it's why he took the job. Eventually he concedes.
Played Straight with some of the Alliance Officers they meet, some are amoral evil jerks, some are just doing their job, and others are chasing after the crew when they break the law. In the movie, Mal even has a conversation with one of the guards when they rob a bank, telling him that if he gets shot, he'll look more heroic in letting the bank get robbed.
Flander's Company: The premise of this French series, where villains are actually paid by heroes to commit evil, fight them and lose.
F Troop: The Hekawi Indians have no time to terrorize the settlers when they're busy making souvenirs for tourists and distilling whisky for the town saloon.
It's also shown that on the rare occasions they do attack, it's at the behest of Sgt. O'Rourke who wants to maintain the reason for the Fort's existence and allow him to continue running his business.
Get Smart: Constantly played this for a laugh. Often when Control and KAOS agents talked during combat, it turned out that KAOS had much better employee benefits.
The Hero Yoshihiko And The Devil Kings Castle: Episode 2 has a literal example with a group of bandits who corner the heroes, only to leave them be when they realize it's already time to punch out for the day. Their leader tries to convince them to stay, at which point the bandits claim their union doesn't allow "overtime" killings.
Mr. Bennet, known in the early season of as 'Horned Rim Glasses' for his eminently clerkly appearance, was a frightening example of this trope played absolutely straight, until a family crisis pushed him into his Heel-Face Turn.
Daphne Millbrook from Volume 3 is another example, an Affably Evil speedster that is reasonably personable around Hiro and Ando, despite pursuing the same prize.
The Man From UNCLE: In the second season episode "The Arabian Affair", we actually see a THRUSH minion in their New York satrap carrying a lunch pail and punching a time clock as he leaves the office. As well, throughout the series the viewer sees numerous uniformed THRUSH forces (usually guarding headquarters and other important facilities), with the implication that these personnel are at least drawing a steady paycheck, if not actually punching a time clock.
Mighty Morphin' Power Rangers: Rita's alchemist Finster didn't really seem evil (proud of his work, maybe); in fact, he seemed willing to do whatever anyone told him, Rita, Zedd, Master Vile, and even Goldar (he did draw the line at listening to Rito, however). He even once quipped, "Sometimes it's no fun being a bad guy..."
The "Mads". While evil and plotting to take over the world with bad movies, they could also make it clear on occasion that there were really no hard feelings. Dr. Forrester would cheerfully swap invention ideas with Joel, Pearl would invite Mike over for a beer and a chat, and their various subordinates were all too incompetent to be really malicious.
This may be a better example of Go-Karting with Bowser; nobody was paying the Mads to be evil (with the possible exception of Frank). That was just how they rolled.
Prison Break: This show is full of punch clock villains. The prison guards like Warden Pope were punch clock villains-Good guys who even had the respect of the audience and the protagonists but were simply in the way of a bigger cause (freeing an innocent man from prison) so they had to be taken down. Same with Paul Kellerman. He was a humongous threat to the protagonists but he was depicted as disinterested in the people he was trying to kill and a man dealing with heavy pressures from his employers. These punch clock villains were contrasted with characters who became emotionally invested in the destruction of the protagonists like Brad Bellick.
Revolution: Major Tom Neville is this. He knows that Monroe's plans will kill lots of people, but he is apparently not bothered by this. In episode 2, he claims to Danny that he doesn't enjoy what he's doing, but this is only order they've got. In addition, his wife Julia is urging him to kill Monroe and take his place as head of the Monroe Republic in episode 8. Episode 11 shows Neville looking a little more excited at the prospect of systematically exterminating rebels than is appropriate. In episode 13, Neville and his wife flee the Monroe Republic when he fails a mission for Monroe. Episode 16 has him working for the Georgia Federation, and enjoying the power he has a little too much. Finally, episode 19 and the first season finale result in Tom Neville betraying the Georgia Federation, taking over the Monroe Republic in a coup, and planning to take over the continent for himself. All things considered, this is a Subverted Trope.
This was how the Klingons waged their civil war, with soldiers from rival sides drinking together in bars at the end of a long day's slaughter. In an interview, Ronald D Moore even cited the classic Looney Tunes Ralph the Wolf/Sam the Sheepdog cartoons as his inspiration.
The Ferengi as well, only doing evil when it gives them money. The crew of a Ferengi ship deposed their captain, who had tried to kill Captain Picard, because "there is no profit in revenge." (There was even another Fereni military officer that appeared briefly in that episode who gave Picard information for free. Of course, that may have been because the villain in question was an escaped convict who was criminally insane.)
The reapers may or may not count, taking the souls of those that have been touched by death in the whatever city they are assigned too. It is highly debatable is what they are doing can really be considered "evil."
Torchwood: Children of Earth: The trope is one of the principal themes. Many characters in the British government fit the trope, none more than Frobisher, designated Butt Monkey and expendable fall guy for every single action taken by his superiors during the miniseries. You feel really bad when he finally kills his family to spare them a Fate Worse Than Death and then commits suicide himself.
Vega$: Vincent Savino may be working for the mob, but he's an outright visionary when it came to casino management. His vision of a new era of Las Vegas casinos include fancy restaurants and boxing arenas to attract the gamblers. He also wanted to buy the Tumbleweed, tear it down, get rid of the sawdust, and create a modern casino using legitimate financing from a bank instead of union pension fund loans. Today he'd be a respected and legitimate casino executive instead of a criminal.