Members of the Hymn of One cult in lonelygirl15 are, for the most part, just religious people who like to meditate, find their "inner song", and do charitable work. Unfortunately, the people in charge have other plans.
Explored further in KateModern, with the character of Steve Roberts. "I was just doing my job!", indeed.
Dr Horrible fits this trope rather well. Sure, he invented the freeze ray and transported gold bullion from a bank vault, but he also does laundry a few times a week and enjoys frozen yogurt.
There's also Moist, who leads a "life of crime" as a henchmen, and spends his free time dating and hanging out with friends in rooms with pink wallpaper and an abundance of stuffed toys.
In the story "Boston Brawl 2" of the Whateley Universe, the Big Bad brings his Quirky Miniboss Squad and also four mercenaries in case the heroes show up. One mercenary, the Anti-Paladin, is appalled that - while they wait for the signal - a couple other of the mercenaries are sitting around playing a videogame. Definitely Punch Clock Villain material.
Ironically, the Anti-Paladin himself is just a professional. He's a bit of a Noble Demon, though still evil. (He sacrifices kittens so he can enter holy ground. However, see his focus in "Angel in Father John's Basement".)
The minions that She-Beast hires in "Saks and Violence" are the essence of the Punch Clock Villain. They're hanging out in a (supervillain) bar before going home for the night. They hire on after hearing what they can earn. They're just out to make a decent living.
Tucker: So I suppose if you're helping us, you're not as mean as I thought.
Tex: I wouldn't say I'm mean; I just get hired to do mean things.
Tucker: Yeah, but you like it.
Tex: Well, I think it's important to enjoy what you do.
Tucker: So... let's say I hired you to kill Caboose. You would still do it, right? Even though you're supposed to be helping us?
Tex: Is this a hypothetical discussion, or should we start talking numbers?
Tucker: Yeah, I don't wanna talk about this anymore.
Just Tex? The setting is one of Grey and Gray Morality - depending on which side's perspective you take, nearly anyone on the show could be considered this trope.
Jeff and Hal of Bowser's Kingdom. They can never catch Princess Peach no matter what.
One example is in Episode 5 when Jeff and Hal are trying to bring Peach back to life. They do so, and then Jeff attempts to grab her (despite having no arms), but Mario shows up in a hot air balloon and saves her in time. While Jeff and Hal go back to break the news to Bowser, Jeff complains that Hal should of parked the copter a little closer.
Probably the most notable example in the Movie, where they disguise themselves as Mario & Luigi. It actually fools Princess Peach, but because they insulted Steve earlier, Steve gets his revenge by spreading the false rumor of Jeff and Hal having other plans for themselves.
And guess what happens at the end? Peach gets saved once again.
While it can be debated whether or not the SCP Foundation is evil, in many of the foundation tales and on some of the SCP articles themselves, it is very clear that the people are just doing a job that needs to be done, even if requires horrible things to keep horrors from beyond at bay. A big problem for the Foundation are people who feel sorry for the humanoid SCPs or the class-Ds, causing containment breaches and deaths.
Diamanda Hagan usually employs minions, who are basically Slave Mooks. But when she's in the states she gets The Omega to do her dirty work for her. Though The Omega is like Yin to Diamanda Hagan's yang.
Gigan has this role in Monster Island Buddies. He constantly ries his best to make friends, but always fails and nobody else seems to like him, not even his fellow bad monsters.
Hedorah also counts as one due to her also being a hooker in Las Vegas. When amongst her fellow bad monsters, she seems pretty neutral.
The Lambsbridge Gang, the protagonists of Twig, are a group of children who were created to enforce the will of an Academy of Evil and maintain their information monopoly. They don't hold any malice towards their targets, and are ultimately motivated by their loyalty to one another rather than any real affection for their organization or creators.
In Curveball, the board of directors (and the employees that are in the know) of Haruspex Analytics. They draw their paychecks, hang out after work, and most have families. This is the same group that ordered the assassination of Liberty, and are killing people in highly unethical medical experiments.
Montoya is both a justified and sympathetic small-time criminal who was really only doing dirty work for a major corporation out of a need for money. The extent of his dirty work can basically be summed up as "driving a couple of stolen vehicles and covering for his partners'' — still illegal, but pretty small compared to said partners. The other crooks he is working with would technically qualify as well, since none of them had any real issues with Dacta Corp. and were simply doing their job because they were being paid.
Even Silencia Venomosa has some traits of a Punch-Clock Villain, seeing as she won't go out of her way to kill someone unless she is hired to do so, and she's really only in it for the money.
Thomas Sanders: Virgil is the manifestation of Thomas' anxiety and fears, and frequently sends Thomas into a panic over things that could potentially go wrong, or what other people could think. However, despite his sarcasm and Brutal Honesty, it's clear Virgil doesn't exactly enjoy this, and hates being the outsider all the time. Over time, Virgil mellows out and begins working with Thomas, and it becomes clear that he really does have Thomas' best interests at heart.