Guybrush Threepwood from Monkey Island. He's clumsy, he has little regard for ethics, and his main reason for saving the world from the Dreaded Pirate LeChuck is to get into Elaine's pants and prove his worth as a "mighty pirate" to the rest of the world. In many instances, he'll have no qualms about ditching or even slightly harming an innocent character to obtain whatever he needs to move forward in his "quest." And, when he finally defeats LeChuck and saves the world, he'll make absolutely sure that everybody knows itnote Even though nobody besides him really cares.
Wasteland allows the player to be this, sometimes veering into Villain Protagonist levels - but considering the Desert Rangers represent the only real force of law in the Wasteland, you're still better than the alternative. Wasteland 2 continues the trend by allowing you to be an utter bastard to the people you're supposed to protect - only this time, too many villainous acts will get you expelled from the Desert Rangers, triggering a shorter, alternate storyline where you overthrow them and take over for yourself.
Magus from Chrono Trigger can almost certainly be considered an anti-hero, and only joins thanks to an Enemy Mine situation — since he only really wants Lavos destroyed, he's willing to join the party. Once we find out about what caused his turn to evil, he softens considerably.
The Silencer from the Crusader series of games. In the first game, the character, though definitely fighting for the good guys, is never rebuked by superiors for wantonly killing civilians with weapons of moderate to mass destruction—though this may be due to his skills being impossible to replace, as he is the only known defector from the corps he served with. In fact, a viable secondary strategy to acquire weapons and ammunition is to kill people to take their money, so you can buy from Weasel between missions. The Silencer never seems bothered by it in the least, possibly due to being both a Heroic Mime and remorseless killing machine who may or may not have been born in a vat. The money feature is removed from the second game, but occasionally it is useful or necessary to kill an unarmed civilian - to stop them sounding an alarm (nonlethal force is not an option in either game), move them out of your way when the AI buggers up and stops them in the middle of a door way with their hands in the air, get a keycard, and in rare cases (most civilians carry nothing) get an energy cube or medkit.
Darkstalkers blurs the line between this and Anti-Villain so much it's scary when you think about it. The guy that officially beats the Big Bad in the first game just did it to take his power into himself. The villain of Vampire Savior is trying to kill everyone because it's the only way demons have a shot at beginning anew. Morrigan is a Horny Devil if ever there was one, but never displays any genuinely evil feelings. Alien Pyron was responsible for killing the dinosaurs and laying waste to thousands of planets, and yet in his Vampire Savior ending, decides humanity's worthwhile enough to keep around. The person who will one day become the leader of humanity is so mentally scarred it'll be a wonder if she doesn't kill us herself. The Yeti guy reeks of being a Boisterous Bruiser, until he reveals his people are going to make war on humanity. There are legitimate heroes, they're just not important.
Ayane from Dead or Alive. She's bound by her duty to hunt down and kill her half-sister Kasumi for running away from the ninja clan where they both grew up, and was also jealous of her for getting all the attention while the others saw her as a "cursed child" due to the circumstances surrounding her birth. In DOA 2 and DOA 3, she's a bit of a loner and a jerk, but in her story mode in DOA 4, she helps Kasumi, Hayate, and Ryu Hayabusa bring down the DOATEC corporation, suggesting that her feelings toward Kasumi may have softened a bit.
Sly Cooper goes without saying. His M.O. is thievery after all.
The hero from Def Jam: Fight for NY fits this trope like a bloodied, torn glove, one with the fingers cut out so it can wear expensive diamond rings. No matter how you make him look or sound, he comes across as being as arrogant as the real-life rappers he fights. He even cheats on his girlfriend with Carmen Electra, if you so choose. He kills three of his opponents outright: Trejo, by throwing him onto the tracks of a subway; Sticky Fingaz, by throwing him into the ring of fire that Sticky surrounded them with; and Crow, by throwing him out a window.
Very common in the Drakengard franchise and its spinoff NieR. The only true aversion to this is Drakengard 2's Nowe, a standard Idiot Hero.
Caim from Drakengard. It's hard to sympathize with someone slaughtering thousands of people. Many games have protagonists that slaughter enough mooks to populate a small city. Caim is a Blood Knight: he likes it. And in the end you still end up sympathizing with the guy as he gets some of the most tearjerking and heartwarming moments in the game.
Zero from Drakengard 3. She was a remorseless mass murderess in her past, is extremely temperamental and violent in the present, and still has no qualms about cutting you down if you get in her way, whether you're a man, woman, child, or elderly. Her goal is to kill the rest of the Intoners because if she doesn't, they will ultimately destroy the world, and she has every intention of committing Suicide by Cop at the end to prevent this. Also, she eventually develops something of a friendship with Mikhail.
Nier, the titular protagonist of NieR, is a man who will go to any lengths to save his daughter from the Shadowlord. He is also very protective of his friends and generally strives to do the right thing. However, he has no qualms about slaughtering Shades by the bucketful, even after he learns they are actually human souls, and he shows No Sympathy towards the Shadowlord when Gestalt Yonah sacrifices herself to save Replicant Yonah, rendering the Shadowlord's actions All for Nothing.
2B turns out to be 2E, an executioner whose job is to kill 9S every time he learns the Awful Truth about the Forever War. She does deeply hate this fact, and wishes for an ordinary life, but is forever bound to her programming.
9S is far and away the most affable of the heroes, but he shows a disturbing amount of Fantastic Racism towards the machines, considering them to be mindless automatons in spite of the overwhelming evidence to the contrary he discovers on his journey. After 2B dies, he goes flying off the deep end and eventually becomes an Omnicidal Maniac who wants to destroy the last vestiges of humanity just to make his own suffering stop.
A2, like Zero, is brash, rude, and temperamental. However, she is fighting to honor 2B's dying wish and protect humanity.
In Overwatch, two of the Offense characters fit this trope like a glove:
Solder: 76 is the Knight In Sour Armor variety. While he attempts to do what he believes is right by finding the people that caused the downfall of Overwatch, there is the fact that he raided former Overwatch installations to steal weaponry in order to accomplish that goal. He's also ruthless and brutal when dealing with criminals, and doesn't hesitate to shoot them to death if it means ridding a city of their influence.
McCree is of the atoning version. He is a former outlaw, and now fights the good fight.
Kratos from the God of War series, despite being the hero of the story, is a sociopathic warrior who has little to no compunction over the numerous lives that he has taken. His only humanizing trait is his love for his wife and daughter. Later, Pandora's influence does help him to examine his actions. He actually seems genuinely regretful when he observes the damage he caused after his final battle. But the franchise must continue and Kratos must slip back to his basic character. In God of War III, he kills gods and titans that he himself is responsible for making evil in the first place. Interestingly, Kratos is pretty close to what antique cultures would've considered "heroic". It could even be argued that in the transition from the second and third installments, he went from anti-hero to villain himself, making him no better than the gods he was hunting down and murdering. Hints of this are shown all over the saga, even in the first game, and after he replaced Ares to become the same, or even worse.
Carl "CJ" Johnson from Grand Theft Auto: San Andreas. Unlike prior GTA protagonists, Carl's main motivation is the protection of his family, avenging his murdered mother, and getting rid of the drug dealers infesting Los Santos.
The stars of the 2 DLC games, Johnny Klebitz (The Lost and Damned) and Luis Lopez (The Ballad of Gay Tony) also fit this.
In XIII, the title character seems to be this way at first; Him being betrayed by the other numbered conspirators and left for dead with no memory. The 13th conspirator was named Steve Rowland and was a military general involved with the plot to takeover the United States. However, you later find out that the real Steve Rowland did die from betrayal, and the character you play is really a capable soldier named Jason Fly. Jason agrees to have plastic surgery to look like Steve Rowland in order to shake up the numbered conspirators and force their hand - making him the Hero Protagonist all along.
Kain from Legacy of Kain is generally considered an anti-hero, having apparently doomed the world and subjugated the human race to the point of extinction, but apparently did so since the original choice would have doomed the world either way and is technically trying to save the world.
Max Payne eventually comes out as a hero (at least in the first game...), but he freely acknowledges that he's not trying to be a good guy about a quarter of the way through the first game. He's way beyond trying to do something good, and is only doing what's left.
Max: There was no glory in this. I hadn't asked for this crap. Trouble had come to me in big dark swarms. The good and the just were like gold dust in this city. I had no illusions. I was not one of them. I was no hero. Just me and the gun and the crook. My options had decreased to a singular course.
He also acknowledges, indirectly, his own choices and course in his life with a simple line in Max Payne 2:
Max: Shooting a gun is a binary choice: either you pull the trigger or you don't.
Muramasa: The Demon Blade: Kisuke. He's the nicer of the two, by the way - Momohime is virtuous enough, but Jinkuro, a master swordsman, possesses her. He's not kind.
Persona 5: in comparison to the world-saving heroes of Persona 3 and the Scooby-Doo-esque amateur detectives of Persona 4, the protagonists of this game are a band of Phantom Thieves operating outside of the law in order to right the wrongs committed by some of the most corrupt adults around.
Shadow the Hedgehog in nearly all the games he's been in and is the quintessential example for the series. He debuted seemingly as Sonic'sEvil Twin, at first appearing to side with Eggman in his conquest to Take Over the World, but was actually carrying out his own plans. Although his actions might have seemed evil, he just wanted to avenge his younger sister Maria by punishing humanity. Later on after some Character Development, he pulls a HeelFace Turn and becomes definitive force of good, however he still maintains his no-nonsense attitude and has no qualms against fighting the rest of the heroes if he feels are getting in the way of his objectives, and remains The Rival for Sonic despite switching to his side.
Another prominent example is Rouge the Bat. Like Shadow, she also debuted as an adversary (in the same game no less), but primarily for Knuckles. She was helping Eggman, with the deal that'd she supply the locations of the Chaos Emeralds, and he would give her a means at locating the missing pieces of the Master Emerald. However, she later turned out to be a Reverse Mole tasked with uncovering Eggman's plan. Her motivation for actions however are purely selfish, she just wanted to be paid in jewels and hates anyone who gets in the way of that. Even this is revealed, she remains particularly shady and has no problem stealing said emeralds for herself.
Even Sonic himself counts as one. While he has his faults, they don't get in the way of his heroism. However, as his own theme song from Sonic Adventure states that he doesn't like to follow others' values or beliefs and lives by his own morals and codes, and always makes his choices based on what comes natural to him by his own feelings. He also has a propensity for a lot of vandalism in his heroic acts. Still, deep down, he will always come out as the hero who saves everyone at the end of the day.
The Star Wolf team in Star Fox started as a generic "evil Star Fox" group, but in sequels, the team becomes more anti-heroic. The removal of the two "scum" characters Pigma (a traitor) and Andrew (nephew of the main villain in Star Fox 64) and the addition of a ladies' man named Panther (who falls in love with a character on the heroes team) gave them an opportunity to work with Star Fox.
Considering the game is titled Thief, it probably isn't too surprising that the protagonist, Garrett, is a vaguely amoral and deeply selfish burglar, motivated almost solely by profit, who seems to end up saving the world only Because Destiny Says So and all his stuff is there. In his defense, the people he steals from are frequently much worse, he has a sense of humour, and his world isn't one given to rewarding displays of nice.
Wario, although debuting as a villain, became an anti-hero in the Wario Land and WarioWare series, even once agreeing to help free a hidden figure from a music box in exchange for getting to keep all the treasure he finds on the way. He also helped Mario, Luigi, and Yoshi rescue Princess Peach from Bowser in Super Mario 64 DS. Although his current incarnation is neither a hero nor a villain, just really, really greedy.
When he's not a villain, Bowser sometimes fulfills this role in the RPGs where he's forced to help out Mario fight off bigger and badder villains. Mario & Luigi: Bowser's Inside Story puts him in the role of having to save the Mushroom Kingdom since he's the only one allowed to be the proper villain in his mind.
Even Mario himself comes off as overly self appreciative and cocksure to the Japanese audience, though this qualification as an anti-hero is more of a cultural nuance.
Dante from Devil May Cry. A guy who just wants to hit the jackpot from cleaning up his family mess, score with hot chicks, and look stylish and cool while getting paid. His heroism is just a default reaction to all the demonic nonsense he has to deal with and with a devil may care attitude may or may not go and deal with it personally, or just leave it to little brats who may or may not be up to his standards in saving the world.
Cecil as a dark knight in Final Fantasy IV is this during the intro, where he kills innocent magicians for a crystal, believing it's the right thing to do for his king. After Mist Cave, as the bomb ring destroys Rydia's hometown, however, he becomes a Chaotic Good at best.
Kain. While Cecil believed what the king told him to at first, after he destroyed Mist he turned around and never looked back. Kain, on the other hand, is possessed by the Disc One Final Boss (Who is possessed by the Big Bad...) several times during the game, and although usually calm and dedicated, shows that he is truly in love with Cecil's girlfriend, Rosa; stealing her several times during the game (while possessed), and showing that he, deep down, would be willing to KILL Cecil just to be with her. He has proved to be able to control his inner demons, though, and is truly a good guy.
Debatable. When Rosa is kidnapped, once, it's by Golbez, who does so as much to put Kain in his place as to humiliate Cecil. While Kain does insist on fighting Cecil while brainwashed, his lines emphasize a desire for recognition and superiority, not violence for its own sake. Additionally, since there's no real hint as to any of these feelings when he's not being brainwashed and based on Golbez's brainwashing as seen in the DS version, though it was written in the original script, it can be inferred that he was susceptible to brainwashing especially because he had no intention on acting on those feelings and had been trying to repress them.
Final Fantasy VI has Shadow, as it's obviously described in his introduction. And who knows if he'd really slit his momma's throat for a nickel like Edgar comments.
Cloud of Final Fantasy VII also counts, for about the same period of time. He starts out on the right side, but only because they sign his paychecks. However, it's still on Disc 1 when he starts to say that he doesn't want to think of any of the party might be The Mole because he trusts everyone.
Squall, of Final Fantasy VIII, who likewise gives the impression of it just being a job for most of the story, at least until Always Save the Girl kicks in. His catchphrase is "...whatever."
Final Fantasy IX has Amarant, who under goes a HeelFace Turn and joins your party purely to observe Zidane, not that he worries about bad guys taking over the world so much.
Lightning of Final Fantasy XIII. She's rather "dog eat dog" in her combat philosophy and is constantly making comments like "Target's a target", "Couldn't shoot, got himself shot instead", and "Nothing personal"; is fully willing to kill "brainwashed" soldiers and actually scolds one of her companions for trying to reason with them as they had no chance of getting any of them to listen; and will whip your ass into shape, extremely harshly if she has to. However, she'll fight off entire armies, demi-gods, gods, whatever she has to if you mean the slightest iota of anything to her (Especially if regards her little sister, Serah) and she'll generally try to do the right thing.
Delita from Final Fantasy Tactics unites the world under his own iron fist by deceiving and killing greedy to evil nobles while outmaneuvering the Corrupt Church attempting to control him. He's quite debatable whatever he's this or Anti-Villain, but at least Ramza never hs to fight him.
Altair from Assassin's Creed I. Kill templars for peace. Also in a mini-objective, Altair saves a citizen by killing the guards that harass them. The Assassin order throughout the series. Their motto even states that they "work in the dark to serve the light". Assassins have no respect for the law, working with the seedier elements of the cities to murder important figures and every guard between them and their target. It's all for the benefit of the people and to stop the evil Templar plots.
The Bard of The Bard's Tale is mostly a Chaotic NeutralJerkass whose primary goal is "Coin and Cleavage" rather than any heroic deed. He's only spurred on by the main quest to save the princess for the opportunity to shag her at the end. This trope is deconstructed in that acting like a hero and Saving the World doesn't benefit him at all. The Evil Ending is the Happy Ending, where he gets to screw the demon princess. And in the Neutral Ending, he's no kind of hero or villain, and gets to party it up with some dancing undead.
Mira, from Knights of the Old Republic 2, has some...interesting...views on how to deal with men, has a well-deserved reputation as one of the best bounty hunters in the galaxy, and has a temperamental streak a mile wide. She also has a deep-rooted respect for life and a strong personal code of honor; sometimes she comes across as an Anti-Hero and sometimes as a more traditional hero. If you choose dark-side options up until the critical choices in the first game and then take the light-side final options, you get a character who looks like this.
The fan-made Neverwinter Nights module A Dance with Rogues forces you to play one to get any even remotely heroic traits into your character, due to the Crapsack World it is set in. The Bastard of Kosigan module has Alexandra de Velan, who is out to take over the titular county and is prepared to kill anyone in her way. However, her hatred of every single member of the ruling family except for Alexis is at least partially justified and her plan if you don't ruin it leaves Alexis alive in a comfortable situation.
Mao, from Disgaea 3: Absence of Justice is the Evil Academy's top honor student, a position acquired by disregarding all of the rules and being as much of a delinquent as possible. He develops into an anti-hero after the "Hero" title he stole starts affecting his mind and his repressed guilt over the betrayal of his father surfaces. Much like with Laharl, he refuses to acknowledge The Power of Friendship in the end.
Just Cause series - Rico Rodriguez, protagonist, will gleefully commit murder on behalf of drug dealers and terrorists if it gets him closer to taking down a dictator.
Dragon Age: Origins - It is very easy to play the Grey Warden as one of these in There is no Karma Meter in the game and there are often good rewards for acting like a greedy selfish Manipulative Bastard. It's all for the greater good though, since your end goal is preventing a horde of soulless Ax-Crazy rape happy monsters led by an insane dragon god from killing the world.
Some of the recruitable characters qualify (Morrigan, Zevran, Sten, Shale, to some extent Oghren, and arguably even Leliana by virtue of being an Atoner). The sequel ups the ante; only Aveline fits a truly heroic mold, and she has strong Cowboy Cop tendencies.
Zero from the Mega Man Zero series toes the line on this, as he isn't afraid to kill whatever stands between him and his goal; even his girlfriend, Iris, although the event scarred him mentally. On the other hand, he's always fought on the "good guy" side and wants to see Ciel (and by extension, X's and Dr. Light's) ideals of peace and coexistence between humans and Reploids come to fruition even to the point he willing commits a Heroic Sacrifice to stop Dr. Weil from destroying that peace. As he said in Zero 4before said sacrifice:
"I never cared about justice, and I don't ever recall calling myself a hero I have always only fought for the people that I believe in. I won't hesitate If an enemy appears before me, I will destroy it!"
In the flash game series Sonny, the titular protagonist is one of these, only saving a mountain village from a cult in exchange for finding his way to a town on a map in the second game. When he first meets the guy who offered to help him perform the above task, his response is along the lines of "Get out my way or die". He also helps out a fellow zombie in the first game who was trying to fight off humans that chase him, immediately fights soldiers in revenge when they shoot and kill someone helping him at the beginning, and hesitates when a traveling companion suggests that they kill a human warrior that just helped them against a common threat.
Veradux: Alright, the Baron's gone. Let's kill this whoopy superhero and leave! Sonny: But why? He helped us. Veradux: Listen Sonny. To them, we're monsters. Now we can either be alive monsters, or dead ones. You choose.
Given the setting, the other party members are anti-heroes as well, one example being outlined above.
Meta Knight from the Kirby series, an Anti-Hero Antagonist. He often opposes Kirby because of the latter's Chaotic Good nature (and the trouble it tends to cause). However, he's not nice about it - he once tries to take over Dream Land because he feels it would be a much better place if he were in charge instead of King Dedede.
If the player chooses so, Cole MacGrath from inFAMOUS can become an anti-hero, and in the second game's evil ending can wipe out all non-superhumans.
Duke Nukem from the Duke Nukem videogame series is the prototype of a badass anti-hero.
Wes from Pokémon Colosseum. He steals Pokémon away from their thuggish owners so he can save them from being mindless killing machines. Oh, and he's an ex-criminal who's about seventeen years old and travels around with his redheaded Sidekick and his Espeon and Umbreon and has an awesome motorcycle. Although he's got a lot of street cred for that HeelFace Turn he does at the start, blowing up Team Snagem's base and riding off with their Snag Machine.
From Skullgirls we have Peacock, a war orphan who suffered severe physical and psychological abuse before being rescued and transformed into an anti-Artifact of Doom weapon. She's violent, psychotic, and considered one of the few capable of destroying said Artifact of Doom. In her ending, she also goes on to destroy the murderous Mafia family behind her abuse.
Valkyria Chronicles III: The Nameless is one whole penal legion of them. They would simply gets in, do the job, and then gets out. All for Gallia. And boy, they don't get paid justly for their troubles. They don't even get their name cleared in the end. Sad.
Agent 47 from the Hitman series, could be seen as an anti-hero, seeing that he is a hitman who will get the job done. But only in that strictly way, as you can play either as 1 target assassin or a full nominal psycho with a gun. In a more storywise fashion, he is pretty moral, for example: The plot of the second game kicks off with him trying to rescue his priest friend from the Russian Mafiya.
Bob from Messiah. He may be an angel and an emissary of God, yet, as Satan himself notes, he has "questionable ethics"... in other words, he has no problem with brutal murder, even of ordinary workers and civilians, and with possessing people against their will and leading them to their death. (Granted, several times the game forces you to do it.) That said, he's still perhaps the most sympathetic character in the game, because at least he cares about humanity, sort of.
Yuri Lowell of Tales of Vesperia ultimately wants to make the world a better place, and isn't afraid afraid to do what must be done.
Yuri: Murder is a crime. I know that. Flynn: And yet, you still intend to dirty your hands? Yuri: Intend to? I already have.
Lara Croft in the Core-designed Tomb Raider games is a hero overall, but she isn't exactly a noble person; In the first game (and the remake), Lara is willing to kill people who got in her way when she tried to claim the Scion pieces and slaughters animals (though they do attack her). In the second game, Lara kills even more animals, though every human she kills are a part of a dangerous Italian mafia. Game three has Lara appear incredibly selfish and greedy; she attacks a tribe and their leader for their artifact, breaks into a U.S. government facility to steal their artifact, attacks security guards in a museum when she broke in to steal an item for someone, and when she tries to escape from Antarctica, she runs into a helicopter pilot and gladly shoots him dead to steal his helicopter so she could escape. Granted, Lara does prevent the artifacts she hunts down from being misused by people who want to use the artifacts for a more evil purpose, but her methods are very immoral at best.
Despite the series mostly focused on tongue-in-cheek humor and parody of Console Wars. Plutia AKA Iris Heart from Hyperdimension Neptunia Victory is definitely a textbook example in Neptunia franchise. She might be lazy but friendly like Neptune, but she's also hiding a sadistic nature as Iris Heart, indiscriminately frightening anyone else, whether friend and foe alike.
The three main protagonists of Knee Deep - Romana Teague, K.C. Gaddis, and Jack Bellet - all tend to fall into this trope, not quite fitting in with their respective careers and tending to be self-interested without much regard for the greater good.
Ayano Aishi from Yandere Simulator is supposed to be a Villain Protagonist, but can be this trope instead if you have her go through the game complimenting all of the students and doing tasks for them while eliminating all of her rivals through matchmaking or befriending while never harming anyone. You can even have her pass out food to other students. Sure, it's all for her own selfish motivation, but she'll have helped out a lot of students and made them feel better about themselves. A good example would be with Kokona's befriending method. You find out that her father is in debt to a loan shark, so you kidnap the loan shark's daughter to force him to free not just Kokona, but all of his other clients as well from their debt, saving numerous people and ruining the loan shark's business while traumatizing his daughter.
Also from the backstory, Tiber Septim, the founder of the Third Tamriellic Empire who ascended after his death as Talos, the Ninth Divine, is remembered as a great hero of mankind. However, according to the more heretical tales, Septim was a scheming, Manipulative Bastard who was not above using assassination or betraying allies when it helped him achieve his goals. He was also a colossal hypocrite, preaching the virtues of faith and chastity while whoring around with a young Barenziah (among others) behind the back of his own wife, then forcing a magical abortion on her once she was with child.
Master of the Monster Lair: Owen and Kate are either Type 2 or Type 3. They're doing what they do for the sake of world peace, but they sometimes use some unscrupulous tactics to get what they want, including forging a letter from the Devil Prince threatening to murder the town mayor, in order to get his permission to build a 10th floor. They also have no problem killing enemies, even ones who offered to spare their lives. (See What Measure Is a Non-Human?, in its page.)