Zarbon from Dragon Ball Z. In contrast to Dodoria, who seems to be a ruthless Psycho for Hire, Zarbon is more sympathetic. In fact, he just seems to follow the orders of Freeza because he says that will kill him if he does not.
Captain Ginyu as well.
Subverted: Mana Tatsumiya, the gun-wielding mercenary shrine maiden from Mahou Sensei Negima!, only pretends to be a Punch Clock Villain; in actual fact, she joined up with the antagonists during a particular story arc because she truly believes in their cause. She's still getting paid.
Canis Niger (the gang of bounty hunters that Negi kicked the crap out of), however, truly qualify. A dozen or so chapters after Negi wrecks them, he runs into them in the bath house, where they promptly reassure him that they won't hurt him unless someone pays them to. The worst that they do is a lot of Skinship Grope, courtesy of their female member. Remember the perverted tentacle guy? It's not a guy. But she still reallyloves boobies.
Tsukuyomi actually starts as one, leaving the battlefield as soon as she earns her pay and acting rather polite even when fighting. But the Magic World arc starts, and we see her taking a horrific shift towards Psycho Lesbianor, better said, Depraved Bisexual...
Also: Demons. Even the one who turned Negi's village to stone is implied to not have done it out of his own will. Or at least to have gotten no pleasure from it.
Saiyuki's Kougaiji and his entourage. They're under orders to kill the main character and take his sutra, but when they haven't specifically been sent after him, they're known to ignore his presence in the area completely or even help him. These ones are quite Affably Evil, and when the two groups do fight, they usually have fun doing it.
Sergei Wang from Mai-Otome is a personable Joe when he's not on the clock. He just happens to work for his much-more-evil leader in order to do what he thinks is best for his country. However, his loyalty to his adoptive daughter Nina trumps that of his boss, and he almost gets killed trying to subvert Nagi's Evil Plan.
In the Get Backers manga, Gouzou "Mr. No-Brakes" Maguruma is somewhere between this and True Neutral. He's the only character who has no problems with Kuroudo "Doctor Jackal" Akabane and Ryuudo "Undead" Hishiki, the former being someone the eponymous heroes can work with if absolutely necessary, but the latter the only opponent they go out of their way to avoid. Someone usually hires him to transport the item someone else hired Ban and Ginji to get back, but he's perfectly willing to loan them his taxi or give them a lift if they ask for it. Ginji reacts with his "happy fans" whenever they see him.
Florsheim in Tentai Senshi Sunred are completely this trope. Sunred himself is a bit of a jerk, so the group has to work around their Monster of the Week's work schedules, see when a good time to schedule a fight with Sunred is, and still talk about life on the side. One-off characters consistently treat "vicious monster working for an evil organization" as a totally normal job.
In the fourth anime season, the Amazon Trio, Quirky Miniboss Squad of the Dead Moon Circus, always longue around their own personal bar between evildoing, drinking, talking about various things, complaining about the stress of their jobs, and generally regarding their villainy as a bothersome intrusion to their circus performing.
Their successors, the Amazon Quartet, are a strange subversion....unlike the Trio, they do truly care about the mission to capture Pegasus; however, it's not for the same reason as their boss....they just want to ride it.
Gets lampshaded by Iron Mouse in the fifth season (episode 178):
Iron Mouse: Today’s business is over now! Are you paying me for overtime?
Iron Mouse: Hey, are you even listening? (...) See you! I’m leaving!
Exit Iron Mouse
Most of the Siberian Railroad from Overman King Gainer, Jaboli, Kajinan, and Enge in particular are usually obsessed with getting promoted for a higher pay.
Porco Rosso has a whole set of these. In fact, every single one of the seaplane pirates that form the closest thing to antagonists that the first half of the movie has is very much a Punch Clock Villain. They all put on a tough show of hating "that stinkin' pig", but as a collective, they're about as evil as a box of kittens and are just out to make a quick buck.
Most incarnations of Pluto from Astro Boy. He has zero enthusiasm for his work, or anything else for that matter, because he was only programmed to follow his master's directions.
Hayate the Combat Butler has a team of three Yakuza enforcers, who, in the first chapter, attempt to capture Hayate to sell his organs and cover his parents' debt. They later meet again after Nagi has squared his debt. The lead yakuza explains that he was just doing his job and admits that he actually likes people like Hayate, going so far as to offer to treat him to lunch.
Gunslinger Girl has Bruno, who works for the Padania by disposing the bodies they rack up. He mentions at some point that ideals are nice, but they don't feed your family.
The Dragons of Earth in X/1999 are not particularly evil after hours, they just happen to be on the opposite side of the Dragons of Heaven. Their goal is one of Well Intentioned Extremism.
In Code Geass, most of the Knights of the Round are Punch Clock Villains. They have no motivations for what they do other than that it's their job and they're good at it. Probably the strongest example is Gino Weinberg, Knight of Three. He is definitely one of the best, but even in combat he comes off as one who fights only when necessary; off the job he's very sociable if a little odd due to sheltered upbringing. There are three exceptions: Knight of One Bismarck Waldstein, a Knight Templar completely loyal to the Emperor, Knight of Ten Luciano Bradley, an Ax-CrazyBlood Knight, and Knight of Seven Suzaku Kururugi, one of the main characters.
"Pokémon only do bad things because Master bad." — Ekans (with Koffing), the original Pokémon of Jessie and James of Team Rocket.
Jessie and James themselves sometimes go back and forth between this and Ineffectual Sympathetic Villain. Some episodes, they seem to simply take the day off to work side jobs like selling food. They usually stop stealing when Jessie enters a Pokémon Contest.
This is probably because Giovanni has given up on trying to make them do or actually accomplish anything, and just let's them roam around (well until he gives them actual jobs later as a reward, which they prove to be surprisingly competent at).
Oh boy, GUN×SWORD's villain group runs on this. So, if they're not planning for a Utopia, they're like a normal family, with The Claw as the 'kind father', Carossa & Melissa as normal twin kids, Fasalina as their Cool Big Sis, Michael as the new 'adopted son' who's trying to fit in (much to Carossa's chagrin), and MAYBE Gadved as their uncle. For some reason, Woo prefers to be left out.
In D.Gray-Man, Tyki would sometimes rather slack off and play poker than work on missions from the Earl. When he's off duty and in his ordinary form, he's a nice guy, even to enemies.
Samurai Champloo features a kindly assassin in the second episode hired to kill Jin but after his employer is killed by another of his own lackies for crossing the Moral Event Horizon he calmly sheathes his blade and walks away from the fight explaining that he wouldn't be paid for finishing the job now anyway.
Arguably, Sloth from the manga version of Fullmetal Alchemist. If it wasn't for the fact that he was created by Father, and is threatened with his siblings' wrath (pun not intended), he wouldn't be even bothered with digging a tunnel around Amestris in the shape of an alchemist's circle, for, well, obvious reasons.
A good chunk of the Amestris military also qualifies, because, despite the repeated atrocities through-out the country's history like the Ishbalan genocide, the manga shows that they are just ordinary people following orders. One of the manga's themes is the fact that good, normal people can still do horrible things.
The chimera working for Kimblee stand out in my mind, since they weren't really so bad after all.
Some members of Baroque Works in One Piece, most notably Mr.2 Bon Kurei. He easily befriended the protagonists before he knew they were his enemies, but later fought them with all he had because it was his job. After his organization fell apart, he allowed himself to be caught to help the protagonists escape.
Miss All Sunday/Nico Robin. On the clock, she did whatever Crocodile instructed, when off duty, however, she seems to do whatever she can to actively help the heroes, including offering an eternal pose to Nanimonai Island and saving Luffy when he was Buried Alive in the desert, eventually joining the crew after Crocodile is defeated.
Although there are plenty of genuine rogues in the Navy, ranging from General Ripper Admiral Akainu to Dirty Cop Nezumi, many Marines are this trope. Most particular of these is Smoker, who is shown from his introduction to actually be a very kind person to those he is not pursuing.
In fact, if pirates (albeit kind ones) weren't the protagonists, he could be considered a good guy; he's proven that he cares more about his view of justice than orders from the higher-ups, to the point that he and his troops allied with the Straw Hats at one point. Two points as of the Time Skip, and much more Enemy Mine-ish the second time.
Captain T-Bone of the Navy is the most heroic character in the whole story, who cares greatly for his troops, offers to use his parts of his cape as a bandage for them, weeps openly whenever someone gets hurt, abhors violence, and has a strong enough resolve that he would chase a train going full speed on foot, through a giant storm, in the middle of the ocean. Zoro cuts him down, since he was standing in the way of their train and was NOT going to move for some pirate.
Aokiji also fits as well. As an Admiral, it is his duty to hunt down and destroy pirates. However, he seems at the very least to be morally conflicted about it. He does his job, but, especially in the latest chapters, seems to half-ass it and apologizes when it actually inconveniences people.
The ending credits of the 2008 remake of Yatterman strongly suggests that the Doronbo (Skull) Gang are of this type with a romantic montage of Doronjo in civilian clothes walking in the rain, window shopping, etc.
In fact, in one episode, they are seen using a punch clock to sign themselves out of there hideout and into their normal lives.
Most of the cast of Black Lagoon fall under this. In the city of Roanapur, anyone who tries to kill you, fails, and survives your retaliation is probably a good business contact. They'll also probably try to kill you again, when the price is right. Nothing personal, Just Business.
The Eiserne Jungefrauen in Umineko no Naku Koro ni are magic-denying witch hunters, but only when they're on the job as Inquisitors. Otherwise, they don't mind innocent magic that is used as an embellishment, as long as it doesn't hide the results of what happens. Dlanor, in particular, has a discussion with Battler, explaining this over tea.
Kyouko, one of the enemy espers in Haruhi Suzumiya, has nothing against the protagonist Kyon, and disapproves of her organization kidnapping Mikuru, though she still took part in the deed. She's a perfectly congenial person as long as you aren't in favor of letting Haruhi keep her godlike powers.
Caldina, pre Heel-Face Turn, in Magic Knight Rayearth. She was just a paid mercenary and did not even know what Zagato's true motivation was - only that it was NOT to take over Cephiro.
In Puella Magi Madoka Magica, Kyubey turns out to be one of these, and is willing to go to some pretty serious lengths in order to meet his "quota" of magical girls.
To further elaborate the point, in the restructured universe after Madoka's wish removes the need for witches, he is much more open and cooperative, but simply states that is because it is the best way for them to work. He even says that, were things the way he'd been told they once were, he would totally behave the same way.
Most of the Card Professors from Yu-Gi-Oh! R have nothing against Yugi or his friends even as they block their rescue mission, and duel Yugi only to collect the bounty placed upon defeating him in the duel (and they don't even try to cheat to win, which is saying something because the amount offered is sizable). The first one is even nice enough to loan her duel disk to Jonouchi after Yugi defeats her. On the other hand, the concept of an innocent girl being sacrificed for their boss' project (assuming they know the truth at all) doesn't seem to trouble them, either.
The Wire Master in Mouse has this, where both he and the main character enjoy a drink together because it was a Sunday, and they didn't wish to work on a Sunday.
Kahlua from Rosario + Vampire seems to be a deconstruction of this trope, with a severe dose of Psycho for Hire. She will take any job, regardless of who she has to kill or the toll it takes on her body, and will not stop unless ordered to do so. Despite this, she hates killing, and she will cry the whole time as she does so.
Most of the Thirteen Court Guard Squad Captains during the Entry arc of Bleach would qualify as this. Especially Shunsui Kyoraku, the captain of Squad Eight.
Later on, Espada member Coyote Starrk is a borderline if not outright example.
Semi of Maoh Juvenile Remix, who, although initially sent to kill the main character, is actually fairly nice to him when off-duty.
This applies to most of the Shinigami in Death Note. It really is only their duty to take humans' lives, and they only truly qualify as "evil" insofar as the occasional decision to kill a human earlier than intended - and doing so to save another is an offense for which death is punishment.
In the original version of Yu-Gi-Oh! 5Ds, Fortune Cup contestants Jill deLauncebeaux and Professor Frank are secretly members of Yliaster. In the dub version, however, this is not true for Jill; he's merely hired help.
In Yu-Gi-Oh! ZEXAL, Gauche and Droite started out as this. (Gauche does seem to love his job, but he's more of a thrill-seeker than anything else.) Droite later became an Anti-Villain, while Gauche became a Friendly Enemy towards Yuma.
There were also the Fallguys, a trio of duelists with a notorious reputation, but who were nothing more than mercenaries (and really not very good ones.)
In A Certain Magical Index, there's most of the members of Academy City's Dark Side, who mostly just do what they are hired to do and lead fairly normal lives when not on a job. Teitoku Kakine is like this most of the time, but if he runs into Accelerator, he'll abandon his job to try to kill Accelerator or at least make his life a living hell.
In La Seine no Hoshi (an anime created to cash on the interest over the French Revolution caused byRose of Versailles) there's Zaral: commander of a French Guards group detached to police Paris, he serves as the primary antagonist, but that's only because it's his job to enforce the orders of the court. As long as you aren't targeted by said orders or don't break the law, the worse he does is a few empty threats. In one occasion he even let the Black Tulip go in spite of him being a wanted criminal and a personal hate for him because the Black Tulip had brought him a much worse criminal, only remarking he was supposed to arrest him too and that it would be easy to do it in the Guards' barracks.