An overheard conversation in Ace Combat X: Skies of Deception shows that at least one Leasath shipman would rather be out fishing than watching the surrounding skies for incoming hostiles. Also subverted in the same game, where someone responding to said shipman nonchalantly tells him that he'll have all the time needed to go fish once Aurelia's been defeated. Several other snippets also show that some Leasath grunts genuinely buy into their commanding officer's desire to see the destruction and downfall of Aurelia.
Ace Combat 04: Shattered Skies has the Erusean "Yellow" squadron, who are just soldiers and not really villainous for the sake of it. They even befriend the San Salvacion people and abhor the Erusean tactics of posting AA guns on hospitals in occupied cities. Thirteen even praises the "skilled enemy pilot" who is winning battles all along the way.
Ace Combat Zero: The Belkan War also has honourable "Knight" enemies. You get the feeling that they wouldn't be your enemy except for the fact that you're in the opposing army.
D'Vil in Antagonist is an actor working for Evil Productions, which specializes in supplying video game villains. Unfortunately, he discovers evidence that the supposedly-scripted atrocities might not be as phony as his employers claim.
In Aperture Tag: The Paint Gun Testing Initiative, we have Nigel, who's really just doing his job. He takes a genuine interest in the player and is glad to see them succeed, but he has no qualms about throwing test subjects into potentially lethal test chambers and sending a test subject to their guaranteed death by incinerator at the conclusion of testing. If the player manages to thwart this, however, he seems very happy to be able to see them off from the facility.
Most enemy Ravens in the Armored Core series fight you because they're paid to do so and vice versa. "Most", because there are a few who have it in for you without being motivated by a paycheck.
Sometimes, Assassin's Creed II uses this. Most guards are Jerkasses who shove Ezio around with little provocation, but occasionally, during plot missions, you may eavesdrop on some of them talking about family and friends, and being normal people whose only problem is serving Ezio's enemies. This is given a Lampshade in the last memory with Jacopo de'Pazzi, where Ezio notes that the two guards who have seized him are just doing their jobs and that he'll spare them if they let him go.
Valara of Baten Kaitos Origins makes it repeatedly clear that she does all the atrocities she does only because "work is work" and she's very committed to it. In fact, as seen in the beginning of the game and the end, should you spare her life, she's actually fairly friendly when there aren't any orders to worry about.
Litchi, provided that you just don't treat her as an utterly selfish and obsessed woman just because of the side she serves, becomes this, Anti-Villain and Token Good Teammate for the NOL. She's only in the NOL to develop a cure for both herself and Arakune, in order to live longer and be with her friends. She made every effort to find other help, but everyone else capable of assisting Litchi refused because they saw trying to cure Arakune as pointless and regarded her as irrationally obsessed. Litchi is very distressed about it, as shown with her desperate ranting towards Rachel. She also has no interest in whatever NOL or Terumi are planning like plunging the world into a state of "World of Death" or forcing upon people the "Truth of Despair".
On a greater scale, we have, well, pretty much the entirety of the NOL, really. Sure, on the one hand, the NOL is a global, oppressive, authoritarian organization that heavily regulates society and imposes death sentences on anyone who opposes them or wields Ars Magus without proper authorization. On the other hand, several of the more sympathetic playable characters in the game are/were associated with it, and almost everyone within it are just commoners who are just trying their best to uphold order and safety in a Crapsack World that is already teetering on the edge of entering an age of complete anarchistic chaos and war. Also, Ars Magus? They are incredibly dangerousat best, both to those who wield them and those around the person who wields them once the wielder goes Ax-Crazy, so it's pretty damn reasonable to heavily restrict the usage of them. All in all, the NOL would probably be a pretty okay organization if it weren't for the fact that it's ultimately run by monsters.
In the Borderlands DLC "The Secret Armory of General Knoxx", the eponymous General is incredibly unenthusiastic and depressed about being sent to Pandora to deal with you, as he was ordered to deploy there by his superiors, and just wants to get everything over with so he can leave. In the final battle, he's actually in the process of committing suicide right as you show up. Sadly, his duty has him disable his suicide guns and fight you like a good soldier.
Borderlands 2 steps up the punch clocks tremendously, with Hyperion personnel left and right complaining about having to fight bandits (i.e., what they believe the player character to be) or bemoaning that they'd nearly paid off their mortgage as they slump to the ground and die. They don't even particularly believe they have good jobs, but there is an undercurrent of thought that being outside of Hyperion on Pandora would be far, far worse for them all around, regardless of how true that actually is.
In Borderlands: The Pre-Sequel!, the protagonists are all hired by Jack to help him in his inevitable rise to power. While most of them end up fitting into this label in some way, Athena, Timothy, and Claptrap are arguably the closest thing, being mostly decent people forced into increasingly morally-ambiguous situations but forced to stick around due to either having no real choice in the matter... due to being literal property of Hyperion (Claptrap and Timothy) while Athena's professional pride forbids her from walking away until her job as a Vault Hunter is officially done.
City of Villains has billboards scattered throughout the urban zones advertising for "Minions Recruiting Agency". It's also stated that, because he knows happy minions are loyal minions, Lord Recluse pays his minions extremely well, his pilots especially, due to their hazardous line of work.
Great Grey Wolf Sif in Dark Souls I is only an adversary of the player because he's guarding the grave of Abysswalker Artorias, who sacrificed himself to save Sif. If you play the DLC before battling Sif (and thus witness those events, as the DLC takes place centuries before the core game), a different cutscene introduces the battle. In that one, the wolf actually recognises the player and lets out a clearly sad howl before he tries to fulfill his duty. Given that he can't be skipped even with Sequence Breaking, it makes the battle all the more tragic.
Of all the factions in Destiny, the Cabal best represent this. The Fallen attack you as pirates or rebels desperately trying to claim the Traveler and City, while the Hive and Vex are indirect agents of the Darkness. In contrast, the Cabal in the solar system are merely a military regiment from a nearby empire who have been sent to annex some technically unclaimed worlds. They don't have any real grudge with humanity and their allies (they attack you because you're technically infringing on their territory) and they have no link to the Darkness (in fact, they may be running from it, just like the humans). They're not even a unified force; arguments and disagreements in the regiment are common, not all of them feel particularly loyal to the empire, and many of them are only fighting so that they can just get it over with and go home, as the empire's rules hold that battalions can't return until they're victorious or ordered to retreat by the empire. The lore tab for Skyburner's Oath in Destiny 2 from the perspective of a Cabal grunt highlights this. The unnamed speaker is loyal to the empire, but not "dulce et decorum est" loyal.
At one point, the player comes across an NSF platoon that is guarding an underground supply route. When the player reaches the platoon commander, he surrenders and gives up without a fight because "he's just a reservist". He explains that, under scary-looking body armour, he's just an accountant, and isn't really big on dying just to protect the supply route.
Most UNATCO troops, as they're unaware that their organization is corrupt to boot.
Prinnies only serve Etna (and presumably others) for less than minimum wage in order to buy their souls' merit back. They count as villains because most Demons (Etna in particular) seem to be evil. They're stated to work in Celestia, home of the Angels, as well. They're treated better there and work off their sins instead of working to raise money. Either way, it ends up with them as servants trying to reincarnate into something other than a Prinny.
Disgaea demons in general are this, and are more prone to Poke the Poodle behaviors while behaving like a Large Ham than doing any actual evil. Valvatorez in particular makes it clear that it is necessary for them to terrorize humans, as the fear they generate keeps humanity in line by making them turn to faith to combat it. When the demons slack off, the world goes to hell.
In Donkey Kong Country 2: Diddy's Kong Quest, Klubba is only threatening until you pay his toll, and then he's polite as can be. He will also comment that he hopes you take down K. Rool because he doesn't treat his crew well.
Zevran says that he's only doing the job he was paid to do when the Warden interrogates him after the botched assassination attempt on the Warden. Subverted in that he was actually a Death Seeker who hoped that you'd kill him.
It is literally against Imperial Law for "casteless" Dwarven Commoners to have a job, so they have to be criminals, technically or otherwise, or they'll all starve to death. The sheer insanity involved with this ironclad law is why The Napoleon murdering his way to the top to break it is considered reasonable. If the Warden is a Dwarf Commoner, depending on how you play your character, they may not like what they're doing, but it's the only thing that will let them buy food for their family.
In Escape from Butcher Bay, the guards mostly seem resigned to their work and as much a part of the system as the inmates. When Riddick infiltrates Pigsville and the Butcher Bay mines, you can catch a lot of them going on about mundane things, grief that Hoxie and Abbot are letting the prison go to hell, and complain they haven't had a shower yet because an inmate broke in there.
In Far Cry 4, Mooks sometimes comment how they wish the war was over so they could stop killing their fellow countrymen. Others mention their families and how they're only in The Royal Army just to get paid.
Billy Kane of the Fatal Fury and The King of Fighters series is a criminal primarily because it's easy money. He never holds any actual malice for Terry Bogard, and his loyalty to Geese Howard is because of the massive amount of respect Billy holds for the man. But at the end of the day, he remains Geese's right-hand man and commits crimes so he can support his mother and little sister.
Final Fantasy VII: The Turks, who even help the heroes defeat a common enemy while "on vacation". Through sheer popularity, they got even larger roles in other games/OVAs. They even Lamp Shade it. At the end of said sidequest, Reno receives a call from Shinra and Elena asks "Was that the company?" Reno replies that it was and Rude asks if they're on. Cloud and the others take fighting stances, but Reno replies "No, today we're off duty," (or "No, today's our day off," if you're playing the PC version) and everyone relaxes. It's also possible to skip the final fight with the Turks entirely. Taking that option, Reno even goes so far as to point out that, by then, "Shinra's finished." Having no real reason to fight outside of orders, the Turks leave peaceably (though Elena admittedly needs a bit of convincing from her fellow Turks).
Gafgarion of Final Fantasy Tactics is a mercenary hired by Dycedarg to murder the princess. Gafgarion kills quickly and efficiently with no regard for whom, but also shows a distaste for fighting any battle when there's "no money in it." At one point, he insults Dycedarg for betraying you, Dycedarg's brother.
One particular Galbadian Soldier worries about losing his paycheck for peeving the presidential body double, as he had wanted the money to buy a wedding ring for his sweetie.
Laguna and co. are also shown to be Galbadian soldiers although we find out later that at that point in time, the Galbadians were the good guys.
More notably, there are two pairs of Punch Clock Villains who appear at several points in throughout. The first pair is Biggs and Wedge, who are almost entirely for comedic purposes, despite being fought twice. Both times they are fought, they are minor fights, and they are later seen to have retired from the Galbadian army due to repeatedly being beaten by Squall and co.
The other pair is Fujin and Raijin, who take on a more serious role, taking control of Balamb Town at one point. They are, however, later shown to go against the villain at the time, Seifer, and try convincing him to stop what he's doing. They are not entirely serious, with Raijin frequently making errors, prompting Fujin to kick him in the shins.
The members of LeBlanc's Syndicate in Final Fantasy X-2 are hinted to be like this. At one point, two of them are heard discussing how neither of them had any options left when they signed on with her. Considering that one of them is a soldier who supposedly died during the Mi'hen Mission two years ago, he's right.
Aranea from Final Fantasy XV definitely qualifies. She introduces herself to the party as a mercenary currently under the employ of Niflheim, and at the end of her boss battle, she stops fighting only because it's quitting time, proclaiming that she doesn't work after hours, before she promptly leaves. Hell, later on the in the game, she even joins the party as a Guest-Star Party Member because of Noctis's interest in acquiring mythril from the Vesperpool, at Ardyn's command. She definitely has nothing personal against Noctis or his pals, she's just doing the job she's hired for.
The majority of bosses in the series that belong to an enemy army, but have nothing to do with the main plot, are straightforward Punch-Clock Villains.
If left unrecruited on the Azure Moon or Verdant Wind routes of Fire Emblem: Three Houses, Ferdinand, Linhardt, Caspar, Bernadetta, Dorothea, and Petra become this. They do not have any hostility towards the Kingdom or Alliance, and merely count as antagonists due to fighting for the Empire. Notably, only Ferdinand actually has to be killed to proceed if not recruited, as they are a commander on a key bridge; everyone else can be worked around. On the same routes, Lorenz on Azure Moon and Ashe on Verdant Wind will fight you out of loyalty towards their superiors (who have sided with the Empire) and harbor no ill will towards you personally. However, provided you recruited them beforehand, defeating them as Byleth will give you an opportunity to have them re-join the party if you decide against finishing them off.
The animatronics from Five Nights at Freddy's. As soon as the clock hits midnight, they'll try to kill you by stuffing you into a suit (it's a lot more painful than it sounds). When the clock hits 6 AM, the animatronics will leave you alone. The reason for this is because the robots have been programmed with a daytime mode, which makes them go to their stages so they can entertain the children. In the second game, The Phone Guy mentions that the animatronics were never programmed with a night mode, which causes the robots to try and find people in the empty restaurant. They happen to find you, but they try to kill you all the same (until six, of course).
In Halo, several species in the Covenant fall into this category, though the games don't explore it as much:
The Lekgolo (aka Hunters) are starfish aliens who don't really give a crap about the affairs of humanoid aliens, and only joined up with the Covenant because it meant that they would have greater access to space travel (and because if they didn't, the Covenant would've blasted them to oblivion). They also fight mainly as battle couples, making killing them all the more awkward.
Most of the Kig-Yar (Jackals) are just mercenaries who barely even give lip service to the Covenant religion. Most of them are still pretty blood-thirsty, making them shades of being a species of Psycho for Hire.
The Unggoy (Grunts) are just enslaved cannon fodder.
The Huragok (Engineers) are extremely pacifistic and just want to help anyone and anything they come across (they even try to stop the war a few times), even if "help" means "repair this weapon for the grunts of a genocidal military cult".
Richter (the rat-masked assassin who breaks into Jacket's apartment, guns his girlfriend down, and non-fatally shoots him in the head) from Hotline Miami is one of these. Upon being confronted by an enraged Jacket in the "Assault" chapter, he genuinely apologizes to him, but reveals that he knows as little about the people who ordered the hit as Jacket himself.
In Jak II: Renegade, members of Baron Praxis's Krimzon Guard can be overheard discussing (among other things) going to see the races during the weekend, having to do sewer patrol after pissing off a commander, and liking the new armor, which is apparently "more comfortable in the crotch."
Ms. Applegate from Kindergarten actually is a genuinely nasty person, but she still hates her job and only works for the Evil Principal who runs the place because he pays her checks. If she has little to no reason to continue teaching, such as there being no students to teach or no principal to get paychecks from, then she books it.
Half of the members of Organization XIII are portrayed this way in Kingdom Hearts: 358/2 Days. They even get vacation days on occasion. Roxas in particular has no idea what he's working for throughout his time in the Organization, and doesn't really take pleasure in his work. Continued in Kingdom Hearts III. Special mention to Larxene, who actively hates the goal she's working towards and is only in it to have an excuse to hang out with a friend who works with the bad guys, and Xigbar, who is literally only in it because he wants to get paid, albeit with a particular artifact, and thinks the whole thing is otherwise ridiculous.
Yuna, Rikku, and Paine, the heroines of Final Fantasy X-2, work for Maleficent in Kingdom Hearts II because she pays well. They switch to the good guys' side only because they think Leon will pay better. Though, after initially planning to take all of Sora's items as payment, they decide not to after hearing about the hardships Sora has endured, and give him a Keychain as a gift.
Pete also counts, as he is fought in a few of the worlds and manipulates the Big Bads of most of the worlds. He isn't really evil. Just incredibly selfish. He's only doing these things because Maleficent promised him freedom on condition of his servitude.
The Magic Mirror from Kingdom Hearts: Birth by Sleep also qualifies. If left to his own devices, his behaviour is quite benevolent, even though he speaks in rather cryptic phrases. It just so happens that he answers to a vain and cruel owner.
The Phantoms in The Legend of Zelda: Phantom Hourglass and The Legend of Zelda: Spirit Tracks are creepy suits of Animated Armor that must be avoided at all costs and can take Link out in one swing of their enormous swords. Zelda can possess Phantoms in Spirit Tracks, though, and can talk to other Phantoms as a distraction. Doing so reveals that many Phantoms regard their patrols as a day job and complain about walking the same paths, patrolling rooms full of lava, and feeling that no-one listens to their opinions on their work. Some even make comments like "Bob quit yesterday. Too hot for him" and "Is it break time yet?".
Lonely Wolf Treat: Frosting is a town full of racist rabbits that cause no shortage of trouble for the main characters, and later on a rabbit named Mousse is hired to guard the town's entrance. Although Mousse's job is to prevent all non-rabbits from entering the town, Mousse himself has nothing against other species and is willing to chat with you as long as you don't cause trouble.
Mass Effect has several enemies whom you can have conversations with, where they indicate that they're just doing their jobs trying to stop you.
In one jarring instance, you can encounter a mercenary commander whose exhausted, wounded, and undersupplied men have spent the last several days fighting for their survival and protecting a large number of civilians from Bee People. After helping him fight off another attack, and then proceeding to clear out the infestation, you come back, only to find he's received new orders: to kill you. He even says in a very tired, sad voice that he's very sorry, but he's got his orders, right before the shooting starts. Fortunately, it is possible to go another route.
At one point in Mass Effect 2, after fighting through a bunch of Eclipse mercs, you encounter a young Asari merc hiding in a room. She pleads for Shepard not to hurt her, claims she has no quarrel with him/her, and thought her job would be "fighting bad guys", not killing innocent people for whatever psycho who hires the team. The Paragon option is to let her go. Subverted when you later find a datapad with a log entry by said merc where she sadistically gloats over having brutally murdered a volus merchant. If you had let her go, the only thing you can do is give the evidence over to the police. You can't find the evidence prior to encountering her, either. She'll escape, leaving her room empty if you try. There is a fairly major clue in that she's wearing the uniform an earlier (optional) conversation mentioned the gang members have to perform a murder to earn.
Hell, even the the Reapers can count as this, given the information from Mass Effect 3's ending. It is revealed that they, or at least most of them (Harbinger's Large Ham suggests that it has at least a semblance of a personality) don't have much free will per se and are merely machines under the Catalyst's control; if you free them in the Synthesis ending or replace the Catalyst in the Control ending, they will in fact aid the Council species in repairing the damage they have caused.
Max Payne and Max Payne 2 love this one. There are quite a few instances of unsuspecting goons standing around discussing their profession. In a late level of the first game, if you postpone the guns-blazing part, you can overhear two Men in Black discussing their work and one of them actually says that it's "just a job from 9 to 5". Quite a few of them consider being allowed to kill people a major perk, though.
Technically all the robot masters from Mega Man (Classic) would count, since they're only following their programming, but a lot of them certainly seem to enjoy their villainy above and beyond their programming and do seem to hold grudges against the titular Blue Bomber. The straightest example is Sword Man from Mega Man 8, who evokes Nothing Personal and Just Following Orders in one of his opening battle quotes.
Megaman Juno from Mega Man Legends. Juno himself is not evil, but his job is to destroy all life on the island when it grows to a certain point. Even when he's defeated, he still has no hard feelings towards our protagonist.
Klaymoor and especially Bola from Mega Man Legends 2 are merely a rival group of diggers out to get the same prize as Mega Man and his crew, to the point where they probably wouldn't even be considered pirates but legitimate diggers if not for their affiliation with the Bonnes and Glyde's crew (though they're apparently Retired Monsters who have mellowed out with age). In fact, Bola doesn't even want the Mother Lode and points out that he has more than enough money to live comfortably for the rest of his life, but is simply in it to help his friend, and both of them pull a Screw This, I'm Outta Here once they decide the prize simply isn't worth what they're going to have to go through to get it.
In Metal Gear Acid 2, the security chief of SaintLogic, Vince, is a terrifying figure in full-plate armour with glowing blue eyes... who is disturbingly nice due to being this, not going out of his way to hinder Snake any further than his job requires, talking to him in a chatty and informal manner, and siding with him occasionally when he feels his job is asking him to go too far. Because of this, he's a soft target for Venus, who is far less nice a person than he is.
Kazuhira in Metal Gear Solid: Peace Walker. Despite being on your side, in that game, you're playing as Big Boss, an eventual villain, and Kaz goads him into doing stupidly evil things like building nuclear weapons, kidnapping people, and (possibly) stitching sharp pieces of metal into his chest. Kaz is actually a pretty nice guy, but his main goal is to make a ton of money.
The enemy soldiers are merely doing their jobs, unlike the enemy soldiers in the previous two games who are, personalities aside, knowingly criminals and/or mercenaries engaged in illegal activities. The final battle against The Shagohod even showcases them in a fairly heroic light, putting their own lives on the line to save their allies from the burning warehouse or the oncoming Shagohod.
It turns out that The Boss was ordered to defect to the Soviets and was the antagonist for most of the game solely so that you could kill this "defector" and be the hero.
In Mirror's Edge, Celleste signed up as an assassin for the corrupt mayor because it's a comparatively safe job that puts bread on the table, and also has the great advantage that the police forces are now on your side, instead of trying to shoot you on sight. As a wonderful example of an actual Punch-Clock Villain, she still hangs out with her friends after work, and drops hints that it really would be better for them to stop antagonizing the oppressive government and start a more socially accepted type of life.
The Pigmask Army from Mother 3 comes off as this way. The guys attend rock concerts, visit diners, make pleasant conversation with Lucas and Co., and in general act like people you'd meet at the office. This is further strengthened when an NPC from your hometown joins the army. He's a pretty nice guy and nothing really changes. Sure, he's wearing the suit, but he's still the same person. On the whole, the pigmasks come off less as minions of evil and more soldiers in a normal army. While there are a few rotten ones among them, and they've got a terrible leader forcing them to commit some atrocities, most of them just seem like ordinary guys doing their jobs as soldiers. In Touhou Mother, they're all Sanae fanboys. However, that game subverts the trope, as they're the unpleasant kind.
In the No One Lives Forever series, random goons can often be overheard by the player talking about their family problems, girlfriends, and office gossip.
The entire point of Papers, Please is that you're a small part of an incredibly large bureaucratic nightmare. Doing the right thing — not splitting up families, letting people through for medical procedures, or keeping out homicidal maniacs with perfect papers — is incredibly hard while also feeding, clothing, and housing your own family.
Pony Island: Although Pony Island was created to harvest souls from the people who play it, Lucifer isn't especially interested in doing so and would rather just make games people enjoyed. He doesn't get frustrated at the player for trying to escape, but he does get frustrated whenever they "fix" his games.
Lucifon of Princess Maker 2 seems to be very much this. When he is defeated in a duel by the father of the game, he points out that it was the God's will that he attack the corrupted land, a point the father can't argue with. He does seem to treat his role more as a job to be done than a chance to act as your typical scheming villain, though he takes a great deal of pride if he succeeds in corrupting your daughter enough to make her become the next princess of darkness either by marriage or You Kill It, You Bought It. He and most of the demons are generally Affably Evil.
The United States Marine Corps in [PROTOTYPE] are just trying to stop The Virus, and are only fighting Alex Mercer because they're told he is a serious threat, which, considering he's a Sociopathic Hero mass murderer who kills thousands of civilians and military personnel over the course of the game, is entirely justified.
Psychonauts has an... interesting version of this. One type of enemy in the mental worlds is called a Censor. Their job is to hunt down manias, waking dreams, and other foreign thoughts and censor them out. Since Raz is technically a foreign entity in a mental world, he's fair game, and you will see Censors being deployed in your general area. Frequently. It's even said that a good number Censors being present is a sign of a healthy mind; the fact that there are none in one character's mind is a sign of just how insane he is.
Many of the Umbrella Corporation employees who aren't Hired Guns or raving lunatics in Resident Evil are this. Many of the Apocalyptic Logs left behind by researchers sway between describing what horrific creatures they've spawned or what terrible experiments they've conducted on innocent people, and telling who won the poker game in their downtime or of their families.
Hideo Shimazu and Kyoko Minazuki start out like this in the first game. Being new teachers in an elite school, they had no idea that their school president is conducting a mass brainwashing plot on the new transfer students that they brought in, they're just doing their job of recruiting. But once the realization hits, they tried to quit, got beaten into submission, brainwashed, snapped back, and turned against the president.
Raizou Imawano, the president himself, is one of these despite looking Obviously Evil, as he's being brainwashed into doing all of this by his nephew and student body president Hyo Imawano.
The Ashura-kai's Terminal Guardian in Shin Megami Tensei IV turns out to be this, as revealed in the Neutral path as part of the Activate All Terminals quest. When you defeat him for the last time, he admits that he was only doing his job to support his family, and decides to finally quit and search for a clean job.
Shovel Knight: Spectre of Torment shows that nearly all the Mooks who serve The Enchantress are this in at least some capacity, most of whom join her because she's offering them some form of compensation rather than that they believe in her cause. The ending even has a scene of various random enemies lining up to receive their paycheques.
Rouge the Bat. She steals jewels whenever she likes and manipulates people to do so, but she's doing it all for herself, and when she's not stealing things, she's just your regular gal who likes a good night on the town.
The Babylon Rogues and E-102 Gamma from the same series. E-102 only tries to kill Sonic out of peer pressure, and the Babylons are racers and thieves.
Orbot and Cubot, Eggman's two robot lackeys, are also an example. Despite working for Eggman, the two are quite friendly and have nothing personal against Sonic and co. In fact, Orbot admires Sonic and would rather work for him than Eggman.
South Park: The Fractured but Whole: Butters as Professor Chaos resorts to these once he runs out of regular minions. Which means he actively hires illegal Mexican immigrants, who are entirely willing to put up with wearing tinfoil costumes and participate in what's essentially just a surprisingly dangerous children's game because a job is a job, and Butters is paying. This also, and rather hilariously, explains why the randomly encountered Chaos Minions begin attacking Butters as well once he joins Coon and Friends:
Butters: Chaos Minions, what gives?! Chaos Minion: Your last paycheck bounced! Chaos Minions want to get paid!
C. Q. Cumber from Splatoon 2: Octo Expansion is the conductor of the Deepsea Metro. Despite working for Kamabo Corporation under Commander Tartar, he's not a bad guy, only "faithful to his duties" as Hisashi Nogami puts it. Even activating Agent 8's Explosive Leash and declaring "test failed" is nothing personal, only a professional adherence to his job protocol.
Shown often in the Splinter Cell series. Sam Fisher will often encounter guards or soldiers who are simply doing their jobs, or are even completely unaware of what they're guarding. Some missions will involve Sam going up against people whom he can't use lethal force against, including American and foreign soldiers, CIA security guards, and the Mexican Coast Guard.
In StarCraft, the Dominion's top Ghost agent, Nova Terra, is this. She's fiercely loyal to the Dominion and does what she is told to do, but she has no personal enmity with her targets. Thus, after Arcturus Mengsk is overthrown and Valerian takes over, she immediately stops opposing Raynor's Raiders as they are integrated into the Dominion's military and government.
Knights of the Old Republic in particular portrays the Sith troops as Punch-Clock Villains, at least on the first planet. When off duty they hang out in a cantina, and on being talked to tell the player character that they're unhappy about being posted on a planet that hates them, also inviting you to a party. When the player character steals a set of Sith armor and talks to the Sith patrolling Taris, they are rhetorically asked "Is there anything more boring than being out on patrol?" Down in the Undercity, one of them is defensive and angry about abandoning some of his people to die on a superior's orders, though he does it anyway. This is probably to enhance the fact that just a few gameplay hours later, Darth Malak destroys the entire planet, killing millions of innocent civilians and his own troops.
In Star Wars: The Old Republic, a light-sided/neutral Imperial player (especially Bounty Hunters and some flavors of Imperial Agent) often comes across as this. They know they're working for a bunch of nutcase Darths and a maniac of an Emperor, but the Empire is their home and they have to look out for their people.
In the Dark Forces Saga, the Imperial Stormtroopers are sometimes seen as this. If they're not aware of Kyle's presence, you can often overhear them complaining about their superior officers and the tedium of guard duty.
Crimson Viper in Street Fighter IV makes it clear that beating the crap out of the world's top fighters in order to assassinate Seth is just business, and she's indicated to be a perfectly friendly person outside the ring who enjoys spending time with her daughter.
Both Teams in Team Fortress 2 are probably Punch-Clocks — whether it's hero or villain depends on your perspective, but since the work they do generally involves the destruction of property, and killing people, and a number of them enjoy it, they're probably closer to the negative side. Despite being highly paid, they are hilariously mentally unstable at best... but they probably wouldn't bother if they weren't getting paid an absolute fortune.
While he is a definite badass, the Sniper seems to think of himself this way. "Sniping's a good job, mate! It's challenging work, out of doors. I can guarantee you'll never go hungry..."
The Engineer, meanwhile, is mostly concerned with "solving practical problems" and self-defence.
The Demoman has tea with his mother in the mansion he bought for her on his days off.
Aemilia in Tears to Tiara 2. She was originally head bureaucrat of The Empire, member of the reform party, and Hasdrubal's ally at court. Now she's an inspector of the ruins of the aqueducts outside Qart Hadast and does the bare minimum to earn a living.
Plenty of them in the Tekken series, as not everyone is that much concerned with the Devil Gene business:
The best example would be Craig Marduk. Yes, he did kill Armor King, but not out of malice or service to someone who wanted AK dead; it was just a heated fight where something went horribly wrong. Despite the incredible rarity of a Tekken competitor killing another Tekken competitor (not even Nina once succeeded, and she's getting paid for that!), Craig has never once crowed or threatened someone else over it. He wants to be the #1 MMA bruiser in the world, and if he has to get by a vengeful wrestler to do it, that's just another day at the office.
The Williams sisters (Nina and Anna) take any job and don't expand it to their personal lives, as their aim is just to settle their sisterly rivalries for good.
Eddy Gordo is only in Jin's army to get the cure for his sickly master.
Bruce Irvin is a good friend of Kazuya Mishima and usually serves him well, but outside his servitude, he's a Friend to All Children and helps them out when he can.
Almost all of the Mooks in TimeSplitters Future Perfect. They almost feel like real people with lives of their own, and one starts to feel a little guilty for having to kill them. Upon beating the game, you learn that you didn't actually kill anyone. Thanks to the magic of time-travel, the events that led up to the Timesplitter War never happened.
The jaegers of the Trails Series. As Rutger, the "Jaeger King" himself explains, they follow the money and go from job to job, no questions asked. One minute, they may be drinking with someone, the next, fighting them.
In Tyranny, Sirin is not especially happy about serving Kyros as the Archon of Song. She helps out the Scarlet Chorus as necessary, but does not hide her disdain for them, and happily jumps ship to the Fatebinder's party when she gets a chance. After the game, if treated with kindness enough to earn her Loyalty, she makes a full HeelFace Turn and goes about the Tiers using her magic to bring peace and hope. If Fear dominates, she goes off the deep end and becomes a bloodthirsty cult leader.
Silver Sable appears as this in Ultimate Spider-Man at the end, when Spidey thinks that she is going to attack him after showing up at a rooftop, but she's not gonna since her contract with Bolivar Trask expired ten minutes ago. When Spider-Man is about to question her about what she's doing, Sable interrupts him by claiming "business is business" before leaving him to get Trask.
Most Reapers from The World Ends with You aren't too sadistic for their job. As a general rule, the Game Masters are usually a lot worse than the Support and Harriers. Kariya and Uzuki in particular stand out. While one Game Master has everyone on standby, you can run into Reapers shooting the breeze or playing Tin Pin Slammer while wondering what's going on.
Support Reaper: Man, today was supposed to be my day off! This sucks. I'm starving! Tell you what, if you can get me a Definitivo Chili Dog, I'll let you through.