Jack Bauer of 24. He's perfectly willing to torture, mutilate, execute allies if necessary, and break nearly every law in the book. To his credit, he does intend to stand trial for any laws he breaks, even though this never actually happens (given that this isJack Bauer we're talking about, perhaps nobody is brave enough to try).
Captain Denniger in Ascension, a serial philanderer who is not above letting his wife sleep with his main political rival to gain an advantage. But he also clearly cares about his crew and ship and is willing to risk his life to save them.
Most of the Colonial fleet counts. While they are the protagonists, they have become much more distrustful and wary after seeing their friends and family murdered in a vicious surprise attack. The knowledge of that the slightest misstep on their part may result in the extinction of humanity lies heavy on their minds, which leads to numerous instances of I Did What I Had to Do. Seeing how the Cylons were quite willing to betray them in the first place and they are quick to adopt a 'fool me one shame on you, fool me twice, shame on me' attitude when it comes to their Cylon allies of convenience. Many of the Cylon-human interactions throughout the series go this way: the Cylons approach the Colonials with "genuine" intentions who state their own terms to make the other side sweat a bit but generally accept the deal... at the front. As soon as they have what the Cylons want, the Colonials instantly turn on them and try to extort even more, at the end of which they summarily declare "You Have Outlived Your Usefulness" and throw the hapless skinjob (who has the blood of several million on his or her hands) into the brig or out of the nearest airlock.
Elizabeth "Liz" Keen from The Blacklist starts to become one after the death of Tom. While being a good person, Liz disposes of Navarro's body using The Stewmaker's MO, after the latter dies of an injury.
Avon of Blake's 7 is a particularly good example: He begins as a mix of The Rival and The Lancer, supporting Blake only when it's in his personal interest and because he wants the Liberator. Later, once he becomes the leader of the group, he becomes increasingly paranoid and sociopathic, at one point nearly murdering Vila in cold blood.
Blake himself was edging into this trope towards the end of the Star One story-arc; he was pressing ahead with a plan that he knew would cause massive collateral damage and potentially kill millions of innocent bystanders, despite being presented with a perfectly workable alternative plan — by Avon no less — that could have achieved the same goals almost bloodlessly. And the Federation were bouncing back from Star One getting blown up by the final season, so he might as well have not bothered.
Boston Legal — Alan Shore is lecherous, conniving, snarky to a fault and one of the most dedicated defense attorneys at Crane, Poole and Schmidt, who routinely does tough cases Pro Bono for friends who need help navigating the law. The best example of his heroism was when he successfully got a man let off for bludgeoning his mother to death with a skillet, and regretted it when the bastard killed again.
Walter White, the main character of Breaking Bad qualifies. A high-school chemistry teacher who is diagnosed with terminal cancer and only little time left. So he decides to start using his degree to make drugs and gather a tidy profit to provide for his family after he dies. By Season 4, he becomes a Nominal Hero by virtue of Gus and Don Eladio's Cartel acting morally worse than him in that Season. Finally, by Season 5, he becomes the Big Bad of his own show, a position he only loses near the end of the series because one of the men he hired turns out to be even worse.
Paige Michalchuk and Gavin "Spinner" Mason from Degrassi: The Next Generation. The two of them are among the most loathsome teenagers ever portrayed on TV, but the audience can still root for them because they suffer far more than even they deserve.
Season 8 replaced them with Holly J Sinclair and Johnny DiMarco, in the respective roles Paige and Spinner held. Neither is a really nice person... but they aren't bad people. Season 10 adds Eli to the mix, who's more proactive about bully problems.
Although the Doctor from Doctor Who is traditionally a Heroic Archetype, some incarnations have been less merciful and more deceptive than others.
The First incarnation of the Doctor, a grumpy old man who kidnaps and deceives his companions, and has to be forced, manipulated or at least asked before he will help. His worst moment was probably threatening to throw Ian and Barbara out the TARDIS in "The Edge of Destruction", something that could easily have killed them. Of course in this incarnation he does get better due to the influence of his Granddaughter and her teachers who he eventually returns home.
Perhaps the clearest example of Christopher Eccleston's Ninth Doctor's anti-heroism appears in the episode "The End of the World", where he prevents the escape of Lady Cassandra and impassively watches as her frame of skin bursts apart horribly, coldly ignoring his own companion's request to heed the villain's pleas for mercy.
For David Tennant's Tenth Doctor, his cold-blooded execution of the Racnoss in "The Runaway Bride" is probably the quintessential example, an act where he lost himself so completely in his own inherent ruthlessness that in an alternate reality where his companion was not there to stop him, it actually cost him his life. Then you have his actions against The Family of Blood. And he brought down the prime minister that led Britain's Golden Age prematurely because of her own ruthlessness against fleeing aliens. All this leading to "The Waters of Mars," where he gets so dark that when he decides to Screw Destiny by saving three people from the monster of the week, one of them (who knew she was fated to die, according to history) walks inside and kills herself.
Not to mention The Brigadier, who ordered the mass genocide of a hibernating race, and aforementioned prime minister Harriet Jones.
The Eleventh Doctor. Some of his darker actions include brainwashing the human race into enacting the genocide of the Silents without their knowledge, and destroying a fleet of Cybermen ships in order to intimidate the remaining ship to tell Rory what he wants to know.
Let's face it, the Doctor has always had anti-hero tendencies in some way or another.
Shown in extreme detail in this  fan made video, highlighting all of 9, 10 and 11's darkest moments. Aptly named Fury of a TimeLord.
The Sixth Doctor was conceived around this idea to contrast with his mild-mannered predecessor. One of his first actions was to throttle his companion, and later an old man, due to an unstable regeneration. He got better over time, though was still willing to kill someone if his life was in danger and would show little remorse for it.
The War Doctor, to the point where the future Doctors basically disowned him from being the Doctor. Their attitude seems to have changed after it is revealed he didn't actually destroy Gallifrey but helped save it.
Speaking of the Whoniverse, Captain Jack Harkness himself is one, moreso in his own show, Torchwood. Then again, everyone in Torchwood is an Anti-Hero.
Anti-Heroes are everywhere in Farscape. While Crichton tries his best to trend towards idealism and pure heroism, even he has done some very bad things in order to do what's right (y'know, like threatening to destroy the entire universe to force an end to a war between the Peacekeepers and the Scarrans). D'Argo and Aeryn are both more pragmatic, but also have a similar nobility and along with Crichton are among the first to give a What the Hell, Hero? (including to each other). Even Zhaan, who the entire crew acknowledges as The Heart of the group, is willing to use her darker impulses to protect her shipmates and Moya.
And then there's Scorpius: Willing to torture, kill, make deals he has no intent on keeping, and is a Magnificent Bastard of the highest order. However it's all for a reason: The Scarrans are something much, much worse and he's a Necessary Evil willing to do whatever it takes to protect the rest of the galaxy from them.
A theme of the TV series Fargo is that the people in Minnesota and North Dakota all project a friendly and polite demeanor, which masks a lot of anger, resentment, insecurities and jealousy.
Lou Solverson: We're friendly people.
Mike Milligan: No you're not. But its the way you're unfriendly ... so polite about it. Almost as if you're doing me a favor.
Malcolm Reynolds demonstrates a mixture of altruism and ruthlessness, along with a powerful loyalty to his crew. When a defeated opponent threatens to hunt down and kill Mal — and by extension, Mal's crew — Mal's response is to kick him into the engine of his ship. He is glad to make use of River'sPsychic Powers, bringing her along on dangerous jobs, but at the same time is willing to risk his life to keep her safe. He has no problems returning a cargo of critical medicines he's stolen once he realizes how badly they are needed, but also has no issue with gunning down murderers and war criminals in cold blood.
Tim Riggins from Friday Night Lights. He's a junior alcoholic, he's slept with every girl at Dillon High, sees nothing wrong with letting his harem of groupies do his homework for him, and usually, when faced with a choice between The Right Thing and The Wrong Thing to do, will pick the Wrong Thing every time. He's been involved in petty theft, has stolen money from a meth dealer, and has picked more than one bar fight. He carries around a huge suitcase full of self-loathing even though he's one of the best looking people on the planet and is a star on the football team, thus a hometown god. Yet, he's incredibly charming and good-hearted, and he'd move Heaven and Earth for those he loves.
After all her losses and traumatizing experiences, Arya is learning to become more ruthless when dealing out death and judgement to those who have wronged her.
Daenerys seems to be sitting at about Pragmatic Anti Hero at this point. As a whole, she has good morals but also a growing track record of treating her enemies with a brutality that would be hard to forgive if they weren't such colossal assholes. Depending on the viewer, this brutality can even push her into Nominal Hero territory.
Jaime, after revealing his heroic Hidden Depths with a few selfless deeds in Season 3, placing him somewhere between a Pragmatic Hero and an Unscrupulous Hero by virtue of the murkier things he's done in the name of family.
Varys is a dark version - an Unscrupulous Hero maybe. He may be interested in the greater good, at least in the long run, but he can also be very unscrupulous, is a schemer, isn't always trustworthy and has a positively terrifying sense of vengeance.
The Hound hovers between Unscrupulous Hero and a Nominal Hero at the end of Season 3 during the Red Wedding where he goes out of his way to save Arya from being slaughtered with her mother and brother (despite there obviously not being a ransom anymore) as well as trying to shield her from the nightmarish aftermath, and is even fully on board with helping her kill a squad of Frey soldiers (so long as she tells him before she tries it again), thus putting him on the "good" side of things. Further, his utter butchery of Polliver's squad in Season 4 seems to be at least partially triggered by how unrepentantly awful they are, on top of their being his brother's men. He moves more firmly into this role after Septon Ray's community is massacred. He's willing to resume his killing again, but targeting people who are far worse than him.
Tyron is a Pragmatic Hero. He's not above being ruthless and manipulative towards his enemies but he's shown many times to be a good person at heart unlike most of his family.
Daario is an anti-hero of the pragmatic kind. He vouches for some ruthless measures when it comes to dealing with Dany's enemies, but nonetheless seems devoted to her cause.
Heroes has a few characters that would fit the bill for this but out of all of them Nathan Petrelli and Noah Bennet really take the cake. Angela Petrelli seemed to fit this as well through Season 3.
Methos from Highlander is old enough to consider chivalry a quaint fad, and has survived for millenia by being ruthlessly pragmatic. He is protective of his friends, but is always looking out for himself.
Dr. Gregory House of House. He has good intentions (most of the time) but he is not a nice man.
Patricia, especially during the first season, where she went to great lengths to find her missing friend Joy. She had a nasty streak, bullying Nina out of an assumption she'd hurt Joy and driving the rest of her housemates away with her rude and obsessive attitude; however, her motivation was fundamentally based in extreme loyalty and fear. Upon making friends with Nina and joining Sibuna, she remained the darkest of the group. Her actions included smuggling Rufus out of a hospital, threatening to expose the teacher's secrets if she didn't get answers, and rejecting Jason's apology in a deleted scene. The later two seasons would keep this as a consistent character trait, but it was downplayed as her role in the story was decreased.
Jerome started off as a Manipulative Bastard who screwed around with his housemates for his own amusement; however, his dark turn didn't truly start until his best friend Alfie joined Sibuna. Feeling lonely, he sought out Rufus Zeno, offering to help him with his goal for money. Once he began to get threatened, however, his attitude cracked and he was forced to turn to Sibuna for help. His actions in the season 1 finale, where he was a temporary member of the team, had him be the one to nearly kill Rufus with sandflies to allow himself and his friends the ability to escape. Season 2 stepped it up, giving him a genuinely heroic goal and a subplot involving Mara and his family. To complete his goal of finding a gem his father had once stolen to return to the school, he was forced to work with Rufus for the second time, unwillingly and at first, unknowingly. Season 3 gave him more Jerkass qualities again, such as cheating on Mara with Willow; however, he once again proved to be a fundamentally good person when he fell in love with Joy and decided not to get in the way of Mara's revenge scheme.
Joy herself was quite dark in season 2. Having spent the entire first season away from the school, she returned being incredibly jealous over Nina's relationship with Fabian, and the closeness of the Sibuna gang. This lead to a streak of poor actions, such as using Mara's blogging alias Jack Jackal to slander Nina, later claiming to be Jack Jackal herself after Mara wrote about Jerome's parental issues, and then turning on all of her friends including Patricia for calling her out on it. However, when Nina fell into the pit during the Senet Game, Joy was more than willing to help Fabian and Sibuna get her back, proving a genuinely decent and compassionate side to her. Season 3 featured her going along with Mara's scheme to humiliate Jerome for revenge, even despite falling in love with him during the process, leading to her breaking his heart to be a good friend to Mara.
Many characters that are The Rival in the Kamen Rider franchise can be said to be this. The first one was Riderman/Yuuki Joji from Kamen Rider V3, and most of the shows that aired from 2000-2010 had at least one Rider that fulfilled this role. As of Kamen Rider Double, the Riders are now largely clear-cut heroes.
In Kamen Rider Gaim, pretty much every rider except the titular protagonist is either an anti-hero or an anti-villain.
Yaguruma Sou/Kick Hopper in Kamen Rider Kabuto, after taking a level in badass. He's still a Kamen Rider, still kicks monster ass on a regular basis (except when he gets so nihilist that he chains himself to prevent himself acting on his impulses to fight said monsters, because that's seeking the light), but claims to be "a loser that walks in the darkness" and is in hell. Plus his hatred for the Designated Hero... and acting on said hatred.
Det. Crewes from Life. On the surface he practices Tao and is into self help materials. Underneath, he has a vengeful Count of Monte Cristo thing going on as he tracks down who was responsible for setting him up when he went to prison for 10 years. Moreover, despite all of his wisecracks during each episode, he always looks like he is going to snap (and sometimes he does).
In Life On Mars, DCI Gene Hunt is a racist, sexist, homophobic, crude, lazy, and borderline corrupt Old-Fashioned Copper who has no problems with taking the odd kickback, beating up a suspect to get a confession or to frame someone 'who has it coming' for a crime they didn't commit. Yet he's still one of the good guys, mainly because even in the grey area where he keeps his ethics, there's still a line — and once it's crossed, he won't rest until the person who crossed it is brought to justice.
Patrick Jane of The Mentalist is normally a straight consultant helping the cops solve murder cases (his tendency to annoy people aside), but he is obsessed with finding serial killer Red John (for killing his wife and child). When it comes to anything involving this ongoing case his rationality and level-headedness flies out the window, his darker side manifests and there are no lines he is unwilling to cross. He fully intends to murder Red John in cold blood when he finally catches him... and partner Lisbon intends to arrest him if he does. At the end of the third season he goes through with his intention and kills Red John, though the episode ends before we find out what kind of consequences are in store for him.
Or at least, killed a man that was kidnapping and enslaving women. He also baited a serial killer into insulting Red John so that Red John would kill him, because he couldn't get rid of him any other way.
All the main characters in Misfits, five young adults with ASBOs, understandably more or less fall under this.
Person of Interest: John Reese. While it might seem clear to the viewer that him and the rest of the team have perfectly good intentions and usually carry them out pretty reasonably (shooting kneecaps as opposed to taking lives when it can be helped, on occasion circumventing the law as opposed to outright breaking it, etc.), him and the rest of the team are definitely this in the eyes of the government and various law enforcement agencies that try to catch them over the course of the show. Well, at least, as far as the good law enforcement officers are concerned. The corrupt ones probably just see them as strong nuisances, if not nemeses.
Lincoln Burrows of Prison Break is probably the best example of that show. His past life was that of a normal thug. In the first three seasons, this was largely overshadowed by more important plot points. However, in Season 4 he seems to gladly show that he's not a nice guy.
Profit's titular character regularly engaged in blackmail, bribery, extortion and intimidation to achieve his nefarious goals. The company he's doing this to is practically just as bad and he only wants to reach the top to destroy what he sees as evil.
Brian Kinney from Queer as Folk is promiscuity personified. He's rude, uncouth, cynical and selfish. He drinks and smokes and uses drugs, he has gigantic daddy issues, has trouble bonding with his son and regularly screws over the people that mean the most to him. But he does love them in his own way, and he makes sure they know that even though he's unable to tell them. And in the end, he's always ready to do what's right even if it won't benefit him specifically.
Revolution: Miles is Unscrupulous after the blackout though he seems to hover closer to Pragmatic, especially after leaving the Monroe Republic though he backslides occasionally.
Neil Burnside of The Sandbaggers is not above lying and cheating to get his way, as both Wellingham and Peele frequently tell him. He even (unintentionally) drives a young woman to suicide in order to prevent her boyfriend from resigning from Special Section.
Cassie is a Disney Anti-Hero after she discovers that she is a witch. She becomes more Pragmatic as the series progresses later on after she discovers her heritage of Dark Magic. When she lets her dark magic overtake her, she becomes an Unscrupulous or Nominal Hero. As the series progresses, although Cassie has good intentions and uses her powers to save people, she also becomes much of a darker individual especially when she discovers her Dark Magic ancestry.
Faye could be classified as Pragmatic or Unscrupulous.
Melissa could be classified as Disney, possibly Pragmatic.
Nick could be seen as Pragmatic, possibly Disney.
Jake starts off as an Unscrupulous or Nominal Hero. As the series progresses, Jake becomes more Pragmatic.
Charles could classify as a Nominal Hero in the beginning. As the series progressed, Charles became more Pragmatic.
Dawn could classify as Pragmatic or Unscrupulous.
The eponymous character from Sherlock. Sure, he assists the police rather than criminals, but he makes it very clear that his primary motivation is to solve cases and relieve boredom, not to do the world any kind of good.
Sherlock: Heroes don't exist, John. And if they did, I wouldn't be one of them.
Sherlock: I may be on the side of the angels, but don't think for one second that I am one of them.
While they still might be the good guys (and guilt whores to boot), both Sam and Dean from Supernatural fit into this category. They're co-dependent, insecure, childish, self-pitying, martyredjerks who've progressively become less disturbed by killing the hosts to kill the demons and other necessary evils.
Castiel and Gabriel (aka the trickster) eschew conventional human morality, but Cas was almost always one of the good guys while Gabriel ultimately ends up behaving heroically. In seasons six and seven, Cass slides down the Anti-Hero scale until he slidesright off.
Bobby!! He might be the most level-headed of the team, but he has his share of flaws and inner demons, and in the rare episodes where the spotlight is on him, he doesn't behave any better than the Winchester boys. In general, The writers seem to love this trope, as most of the hunters and "good" guys fit it to some extent: John (if you aren't too disgusted at his treatment of Dean, Ellen, Crowley ( at the end of season five), The Ghostfacers, that tech wizard who slept on the pool table at Jo and Ellen's bar, Kubrick and Walker.
Tom in Survivors. He stabs a prison guard to death in order to escape before joining Abbey's group. Later he kills an unarmed man by firing point blank at his chest with a shotgun, simply to send a message to the groups pursuers. And yet, he risks his life for the other survivors time and again, and for the most part seems willing to follow Abbey's lead.
Derek Hale from Teen Wolf. Having his entire family murdered by a member of a self-appointed family of "hunters" (his girlfriend no less) has left him with some rather understandable issues. Yet he is actually fairly responsible for a werewolf and is as often a good guy as a bad guy. Sometimes both at the same time.
Terminator: The Sarah Connor Chronicles — Cameron, Sarah, and Derek Reese fit under this =- Cameron especially, as she is entirely willing to kill people who may be a potential threat to the Connors, and in one case used a man who knew important information on the promise of helping him, and then casually walked away when mobsters came to kill him. Derek also has no qualms with killing people who may be a threat or bring about SkyNet's creation. And (legally, at least) all three are terrorists.
Malcolm Tucker in The Thick of It. He started off as the arch-enemy of the main character, then was made the main character, when the writers realised an amoral spin doctor is a far more entertaining character than a worn-out middle-aged politician.
This very first one was Ultraman Agul and his human host Hiroya Fujimiya from Ultraman Gaia. Like protagonist Gamu/Ultraman Gaia, Fujimiya opposes the alien forces of the Root of Destruction that seek to annihilate Earth. However, unlike Gamu, Fujimiya is only protecting Earth itself and not humans. He believes they are also a threat to Earth and plans on eventually dealing with them too. This changes about halfway through the series when he discovers the Big Bad had deceived him into believing he had to destroy the humans, though he still maintains his colder attitude in comparison to Gamu.
Ultraman Justice from the Ultraman Cosmos movies. In his first appearance, he helps Cosmos defeat the second movie's Big BadSandros, but when he returns in the third movie, he is now fighting Cosmos to destroy life on Earth after learning of a prophecy that the planet's inhabitants will become a cosmic threat in the future. Justice himself explains that unlike Cosmos, who has dedicated life to protecting living beings, his priorities lies in maintaining cosmic peace and order without regard for lives. As far as Justice is concerned, it doesn't matter whether you're good or evil, if you're a threat to peace and order on a universal scale, he will search and destroy you.
The first ten episodes of Ultraman Mebius had Hunter Knight Tsurugi, an armoured Ultraman driven by vengeance against the first Big Bad Bogal for devouring the inhabitants of a planet he failed to protect. Tsurugi is so consumed by his desire for revenge that he thinks nothing of side casualties, perfectly willing to hurt humans and Ultraman Mebius if it brings him closer to defeating Bogal. After the defeat of Bogal, he is redeemed and becomes Ultraman Hikari, but as explored in Episode 35, his actions as Tsurugi mean the people of Earth still distrust him.
Ultraman Ginga S introduced Shou, the human host of Ultraman Victory and foil to Ginga's host Hikaru. Shou is a lot more belligerent and harsh towards others than Hikaru, even when those people are against the same enemies as him. However Character Development helps him mellow out.
The military team from The Unit. They are a representation of real world US special operations soldiers like Delta Force, Seal Team Six, etc. They are highly trained, efficient, and ruthless. They will do anything needed to complete their missions. Although they operate by some rules and moral codes, they are trained to do things that the average person would not have the stomach for.
The Vampire Diaries's Damon Salvatore served as unpredictable villain to a reluctant anti-hero as the series went on to Season 2. He usually only did good acts either for his brother's sake or Elena's, the girl he fell in love with. However, through his relationship with Elena, while he is still well-known for his morally questionable actions and believes in "the ends justifies the means", Damon softens and adopts a fluctuating persona between Anti-Hero and Pragmatic Hero from mid-Season 3 and Season 4. He covers this up with indifference or sarcasm, when deep down, Damon really has begun to care.
Elena: "Why won't you let anyone see the good in you?"
Damon: "'Cause when people see good, they expect good. And I don't wanna have to live up to anyone's expectations."
Damon and Stefan's old flame, Katherine Pierce, also demonstrates many qualities of an anti-hero. She's suffered from years of loneliness and is often characterized as being somewhat diabolical, prone to focusing on only her own survival. However, over time, Katherine shows her rare signs of humanity and compassion when she repeatedly saves Stefan, Damon, and bonds with her daughter. She even admits she wants to change. Yet, old habits die hard and Katherine still falls back on her default bitchiness and selfish tendencies from time to time.
Daryl Dixon from The Walking Dead comes across as a foul-mouthed redneck with little consideration for others, yet he saves T-Dog, whom he hates in the second season premiere of the show and has a Moment of Awesome in the process.
Recent episodes have been painting Rick Grimes as Pragmatic with a hint of Unscrupulous, as he seems more and more willing to pull the trigger if it means keeping the group safe.
Omar Little also counts. He robs drug dealers, has killed others and his actions have lead to other's deaths. But he lives by a strict code and will never harm someone who is not in the game. Hell, he never curses in a show filled with foul mouths