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Zevran, of Dragon Age: Origins, 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.
The Warden, if you played as 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.
Though not indicated in-game, the Lekgolo (aka Hunters) of Halo are this. They're 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 Kill Sat them to oblivion. They also fight mainly with battle couples, making killing them all the more awkward.
Most of the Kig-Yar (Jackals) are also just mercenaries who barely even give lip service to the Covenant religion. And the Unggoy (Grunts) are just enslaved cannon fodder.
And the Huragok (Engineer) who 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".
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's 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, the Pigmasks are all Sanae fanboys. Subverted, 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 Turks in Final Fantasy VII, 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.
Most of Shinra Inc actually. Crisis Core in particular makes clear that almost everyone in Shinra is just doing a job.
In Final Fantasy VIII 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 found 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.
The majority of bosses in the Fire Emblem series that belong to an enemy army, but have nothing to do with the main plot, are straightforward Punch Clock Villians.
The Special Forces and Vigoorian Military in the Updated Re-release of Ninja Gaiden. At least, it is implied, but since we never get to see things from their perspective the effect is dulled somewhat.
Megaman Juno from Mega Man Legends. Juno himself was not evil, but his job was to destroy all life on the island when it grew to a certain point. Even when he was defeated, he still had no hard feelings towards our protagonist.
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 who he can't use lethal force against, including American and foreign soldiers, CIA security guards, and the Mexican Coast Guard.
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.
Max Payne loves this one, in both games. There are quite a few instances of unsuspecting goons standing around discussing their profession. In a late level, 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".
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.
Army of Two does this twice, with the People's Liberation Army pursuing the eponymous two mercenaries for blowing up their very spiffy bridge and killed a US Senator in the process, and in the final mission, where Salem and Rios end up fighting the other mercenary contractors of Security And Strategy Corporation, who believe they intentionally killed said US Senator.
Various Star Wars video games have this. 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 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.
Mass Effect has several enemies who 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.
Hell, even the the Reapers can count as this given the information from Mass Effect 3's ending can count as this. It is revealed that they , or at least most of them (Harbinger's  suggests that it has at least a semblance of a personality) don't have much free will per se and are merely machines under theCatalyst'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.
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."
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.
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.
Gafgarion of Final Fantasy Tactics was a mercenary hired by Dycedarg to murder the princess. Gafgarion kills quickly and efficiently with no regard for who, 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.
In Disgaea, 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.
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.
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 Punchclock 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 starting a more socially accepted type of life.
Every character in Iji, even General Tor, the Final Boss and supposed Big Bad. In fact, the only ones who are evil are the General Ripper leading the Tasen, Blood Knight Iosa, and the pyschopathic Asha. The real Big Bad is implied to be the Komato government. And that government is itself a Punch Clock Villain because it's just doing what is demanded of it - exterminating what the shortsighted general public sees only as a threat. It's a pretty dark game...
Half of the members of Organization XIII are portrayed this way in Kingdom Hearts: 358/2 Days. They even get vacation days on occasion.
Also, Yuna, Rikku, and Paine, the heroines of Final Fantasy X-2, worked for Maleficent in Kingdom Hearts II because she paid well. They switch to the good guys' side only because they think Leon will pay better.
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.
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.
At one point in Deus Ex, 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.
In the Borderlands DLC "The Secret Armory of General Knoxx", the eponymous General is incredibly unenthusiastic about being sent to Pandora to deal with you, 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.
Borderlands2 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 Sonic the Hedgehog, Rouge the Bat could be classed as a Punch Clock Villain. 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.
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 has expired 10 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.
In the first Rival Schools, Hideo Shimazu and Kyoko Minazuki start out like this. 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.
And 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.
Hyo is being brainwashed by the spirit of his dead father, Mugen Imawano.
Sometimes, Assassins 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.
Rocket grunts from Pokémon are these. Galactic grunts can also fall under this category.
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.
The other example in Metal Gear 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.
Metal Gear Solid 3 also has The Boss filling this role. It turns out that she defected to the Soviets and was the antagonist for most of the game solely so that you could kill this 'defector' and be the hero.
Cynthia Charleston from In The 1st Degree could qualify as this (as well as being an Amoral Attorney). She is a defense attorney who is defending a man charged with first degree murder and grand theft. However, since the game does not show her or her personality when she is off-duty...
In Jak II: Renegade, members of Baron Praxis' 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."
In BlazBlue, Litchi, provided that you just don't treat her as an utterly selfish and obsessed woman just because the side she serves, becomes this, Anti-Villain and Token Good Teammate for the NOL. She's only in the NOL for the cure of both herself and Arakune, in order to live longer and be with her friends when everyone else refused to help, and is currently 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, opressive, authoritarian organization that heavily regulates society and imposes death sentences on anyone who opposes them or wields ArsMagus 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 fucking dangerousat best, both to those who wield them and those around the person who wields them, 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.
Plenty of them in Tekken as not everyone is that much concerned with the Devil Gene business. The Williams sisters (Nina and Anna) takes any job and wouldn't expand it to personal lives, their aim is just to settle their sister rivalries. 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.
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 competitior 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 have to get by a vengeful wrestler to do it, that's just another day at the office.
Valara of Baten Kaitos Origins makes it repeatedly clear that she does all the atrocities she does only because "work is work" and is 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.
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.
Billy Kane of the Fatal Fury and 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.
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.
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!
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.
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.