The Monarch's henchmen, particularly #21 and #24, are losers and social outcasts who are just trying not to get killed. In one episode, #24 is overheard to complain that working for the Monarch was the only job he could get after the factory he worked at closed ("It was either this or the Army"). In another scene, they both try to recruit new henchmen by searching for out-of-work deadbeats in need of a paycheck. They accidentally hire a bunch of hardcore gangsters they can't control.
Over the course of the show, it's revealed that both heroes and villains are really just bored idle rich people who use their wealth to live a fantasy lifestyle. The Guild of Calamitous Intent keeps the battles from getting out of hand with a laundry list of rules and regulations. Arch-nemeses are gained by an interview process rather than personal vendetta. Battles are sometimes even scheduled like play-dates. Anyone who doesn't play by the rules is rounded up by the Guild, and anyone who is legitimately dangerous is taken out by the secret group Sphinx.
The inversion to the rule might be Monstroso, whose day job as head of a corrupt and powerful law firm actually makes him more evil than his arching after hours.
Ron, from Kim Possible, once stumbled into a bunch of Dr. Drakken's goons in what appeared to be an employee's lounge, suggesting that they're all punching a clock somewhere too. (At one point, Drakken mentions he holds an employee picnic for them.) In a further parody, one of the episodes features a trip to Henchco, a temp agency that does nothing but supply henchmen (and equipment) to aspiring villains.
At some point, all Kim Possible villains have had some version of a punch-clock villain. One went so far as to involve Kim and Ron in a fight between punch-clock villains and punch-clock spies.
Even Shego clocks off for the weekend if they're still in the planning stages of the Evil Plan.
Or at the end of the (inevitably failed) plan, unless Drakken drags her to Karaoke Night (where the civilians politely clap as Drakken sings; yet another example of an off-duty villain).
Fortunately, while Drakken's an incompetent villain, he's a pretty decent boss to work for; when Shego took a Christmas vacation in "A Very Possible Christmas", she was surprised to learn that Drakken had footed the bill for her vacation, including hotel accommodations and meals.
When Drakken gets a cold that's going around, his temporary partner-in-crime actually hires someone from a temp agency. The guy gets into his job, seeing new career opportunities around every corner.
Shego calls in sick, and while she's off the clock, she stands there watching as Ron hauls away the MacGuffin.
Homer unwittingly ends up working as a Punch Clock Villain for megalomaniac CEO Hank Scorpio in The Simpsons. When Hank mentions he's "having problems with the government" (actually a full-scale base invasion straight out of James Bond), Homer expresses sympathy, but doesn't join in the fight (though he earlier prevented the escape of "Mr. Bont").
The Shocker started out like this in The Spectacular Spider-Man. He was a Hired Gun, who seemed fairly honorable. After his initial defeat, his grudge against Spider-Man seemed rooted in his wanting to do the job he was paid to do.
Also, Sandman, who maintains his lack of a villainous nature from the comics. He's only in it for a "big score", not all the vindictive vendettas most of the other villains have (he often says how much he hates revenge), and generally tries not to hurt anyone (except Spiderman and the cops) when on a job. This becomes even more clear in a recent episode, where he, while waiting for a contact, helps a kid get rid of some bullies, and, after accidentally setting an oil tanker on fire in a fight with Spiderman, helps save the crew, and almost kills himself containing the explosion.
Many Fire Nation soldiers are portrayed this way in Avatar: The Last Airbender. Although there are some that seem to enjoy being cruel, most are just normal people doing their jobs.
As well as Ty Lee and Mai, who are only doing evil due to being intimidated into it by Azula (Ty Lee) or being bored and needing something to fill time (Mai.)
Certain episodes show that the Fire Nation Soldiers, by and large, don't even view themselves as Villains. The Fire Nation uses very liberal amounts of propaganda on the populace, and many are convinced that the war they're waging on the "lesser nations" are in their best interests.
In one of the final episodes, Sokka manages to take over a ship from the Fire Nation Airship fleet, by dumping the soldiers into the sea. During a conversation between 3 soldiers, they are portrayed as decent people...who were on their way to burn an entire country.
In Metalocalypse, Dethklok's manager, Charles Foster Ofdensen, is quiet and restrainedly affable, but will kill or torture anyone threatening his "bread and butter". Given that Dethklok are unambiguously a force for evil in the world (though a popular one and only one of a few), and he also doesn't care how many people are killed or maimed by Dethklok as long as there will be no untoward consequences for the band and his job, I think he qualifies as a villain.
Every antagonist (Revengeancers not withstanding) on the show falls into this category, one way or another; Even the Tribunal is only out to get the band because they challenge the status quo and it's their job to maintain it.
Lemongrab of Adventure Time is a tyrannical ruler who sends everyone to the dungeon for a million years. When he doesn't have a considerable position of power, however, he's just your average, mentally unstable, run-of-the-mill jerk who's only a threat to himself. He only acquired that position of power because it was his duty, not because he wanted to. And we all saw how eager he was to be there...
Mixmaster and Scrapper in Transformers Animated worked for Megatron because he had the better oil, and because he didn't try to scare them off. They really had no vested interest in Megatron's cause, and were only really motivated to fight when Starscream shot their oil. With their construction worker theme, it wouldn't be surprising if they used a punchclock.
Furthermore, they started out as friends to Bulkhead, one of the Earth team Autobots, and in "Human Error, Part 2", Scrapper joined up with Sari's group of Substitute Autobots to break Soundwave's brainwashing of the "first-string" Autobots.
Several Looney Tunes shorts where Ralph Wolf is trying to steal sheep away from Sam Sheepdog. There is an actual punchclock in this one, and both the wolf and dog punch in and out at sunrise and sunset. They also get an hour long lunch break, during which they eat lunch together and occasionally have a smoke (probably the reason why television doesn't show these anymore).
Like many cartoon series, it took some tweaking to arrive at the formula. In the first one, only the sheepdogs punch the time clock, a new shift continues pummeling the wolf. In the second, both the wolves and sheepdogs punch in and out, but at separate clocks - no interaction off work. By the third, the two would greet each other at the clock, and by the series end, they even shared a house!
"Good Morning Sam" "Good morning Ralph"
Taz replaced Ralph when Sam resumed his role in a Taz-Mania episode.
Jack Spicer begins to cross into this territory during the second season premiere of Xiaolin Showdown, after a temporary alliance with the heroes comes to an end. When Omi pleads with him to not return to evil, Jack sighs and says that, though he's still going to fight them for control of the Shen Gong Wu, he promises they'll go out for ice cream sometimes when they're all off the clock, which cheers Omi up.
Dr. Doofenshmirtz's evil plans are a routine; he usually won't even start trying to use his newest invention until his arch-nemesis (and best friend) Perry the Platypus shows up to foil him, and he seems to realize that he usually loses. He also has a teenaged daughter who lives with him part of the time; she fits this trope too, though far less enthusiastically, as if assisting her father were simply a normal chore. His plans usually involve creating potentially evil devices for silly, petty reasons.
Suzy is only mean to Candace whenever her brother's around (since she threatens her control over him), and is nice when she's "off the clock."
Buford refers to himself as a bully, but spends free time with his usual "victims" if there's no major bullying to be done.
The Justice League episode "Flash and Substance" has Captain Cold moaning about how crime isn't paying enough for him to make his mortgage payments.
The Mukhtar from Aladdin, an assassin who specializes in hunting down and killing genies. Not because he has anything against them personally (although that may have been the case in the past). Nowadays, he does it because that's simply what Mukhtar do; it's the only purpose for him. He's actually The Last of His Kind, and is now Only in It for the Money. In his second appearance, makes a full Heel-Face Turn after Genie saves him from a Man-Eating Plant.
Strike breaking lowlife Scab on Minoriteam is really just trying to feed his kids with villainy. And the Black Coq works for the White Shadow because he has nowhere else to go after losing his family and restaurant.
General Molotov on Jimmy Two-Shoes is pretty friendly whenever he's off-duty. This is especially notable since he works for Lucius.
Samy isn't really a villain, but since he works for Lucius he counts as this.
A sketch on Robot Chicken featured Jason Voorhees eagerly awaiting Friday the 13th, where he went on his normal killing spree. The following day, he is disappointed to go back to a normal routine.
An episode of Cow and Chicken had Chicken trying to confront a bully on the weekends. The bully says he only bullies on the weekdays and spends the weekends helping the poor.
From Gargoyles, Pack member Dingo is pretty clearly just there for the paycheck, and gets increasingly disgusted with his teammates as they slip further into Psycho for Hire-ness. Ultimately, he decides he's had enough and has a flat-out Heel-Face Turn.
In one episode of Sealab 2021, Sparks reveals himself to be a madman bent on world domination, and offers Marco a position in his organization. Marco considers the job, depending on the benefits package.
Hinted at in a G.I. Joe episode, when the heroes search a COBRA office and one of them, reading some documents, remarks "Hey, they've got a dental plan!"
Later played straight in a profile book, where it's revealed that the vast majority of Cobra's blueshirt grunts were perfectly ordinary people who simply wanted a better life.
In South Park, Satan is portrayed in this fashion. He is also rather meek, insecure and Affably Evil, certainly less evil than Cartman, and chats pleasantly and enthusiastically with his victims (who appear to only be truly bad people) after torturing them.
Ramon: Then why are you working for Castro? You know his stance on homosexuality!
Charles: Because, commie, I have something called a "mortgage."
The villain of "Movie Star" also counts. She even briefly considers not carrying out her duty as a sleeper agent until she remembers that the Soviets said she'd get to direct...
Young Justice has a strange example in Lobo's cameo: he arrived on Earth searching for his mark, beated up the guards, Batgirl and Wondergirl because they were in the way, showed Batgirl and Wondergirl that the guy they were protecting actually was an alien spy, and then left with his mark and no ill feelings.
Space Jam features the Moron Mountain workers who get supercharged by stealing some NBA All-Star players' skills from a magical basketball. Despite maintaining a fanatical devotion to their stogie-chomping boss, however, this trope gets subverted in the end: