The Argent family on Teen Wolf. While their side occupation as werewolf hunters was originally motivated by protecting humans from werewolves, it has developed into full-blown sadism. They are willing and eager to kill werewolves whether they actually pose a threat to anybody or not. The family and their fellow hunters have also expanded their crusade to cover killing any humans associated with werewolves (such as the non-wolf members of the Hale family) or who simply impede their hunting activities. They have also developed a fondness for inspiring fear, and seem to enjoy torturing their targets before killing them. In order for Gerard Argent to take over as principal of the Beacon Hills high school, the Argent's abducted and tortured the current principal, who was wholly unaware of werewolves, just to create a vacancy in the position.
King Uther Pendragon in Merlin tends to come off as one of these. He's a ruthless Knight TemplarJerk Ass who blindly hates magic, seems to have two forms of punishment for those who transgress against him ("Put them in the stocks and throw fruit at them" or "Chop off their head") with little room in between, and has put children to death for fear of their magical heritage. He also clearly loves his son Arthur, is very protective of his ward Morgana, respects his old friend Gaius, cares about his kingdom, and pets the dog on several occasions. He's a villain, but even the good guys realize things would be worse without him there to keep order — despite his extreme methods.
Many of Camelot's enemies are this, too. They're only the way they are because of how their kind has been treated for many years.
The series is also notable for its sympathetic portrayal of Mordred, particularly when contrasted with Morgana's sadistic, selfish evil.
Keamy was a deliberate exception, an effort to create just one character who is pure evil and knows it, setting him apart from the other characters. Nearly everyone else has abides by Grey and Gray Morality, though.
Every single vampire on True Blood. While some of them are not unwilling to perform the occasional good deed, by and large they all seem to be willing to kill, torture, mind control and otherwise abuse the human population despite their public relations campaign about wanting to "mainstream" and live peacefullly with humans.
Brother Justin Crowe on Carnivale. His character development is given equal screen time as the Designated Hero, and (especially in the first season) he's presented as genuinely wanting to do good, but being somewhat hampered by the fact that he's, you know, The Antichrist; it takes some rather extreme measures on the part of his Knight Templar of a sister to get him to stop worrying and love the dark side.
So, so many on The Wire, but probably the best is Wallace, who is only part of the drug trade to provide for his brothers and sisters, grows disillusioned after witnessing a murder for the first time, and later attempts to pull a Heel-Face Turn and get out of the drug trade by informing the police about the finer details of the Barksdale crew. He gets a bullet in the head for his troubles.
Alex Mahone on Prison Break. An FBI agent gone bad, in Season 2, he's blackmailed by the Big Bad into hunting down and killing the fugitives one by one. While he does so with nightmarish competence, his heart isn't in it, and the conflict with his better instincts drives him to drug addiction and near madness. He also loves his son and ex-wife and desperately wants to return to them.
Also, Abruzzi after the incident with the killed child, which gave him nightmares and hallucinations of Jesus. He found faith in Christianity, but, at the same time, couldn't separate from his evil ways and his revenge on Fabonacci. Right before he dies, he actually prays, "forgive me".
Lt. Jon Kavanaugh on The Shield. By all means, he should be the good guy, considering that he's going after Vic and the Strike Team for police corruption and the death of Terry Crowley, but his methods are so thoroughly repulsive and immoral that it becomes impossible to sympathize with him, especially as time progresses and his obsession with catching Vic gets worse and worse. It gets to the point where he's willing to plant evidence in order to frame Vic, which ends up getting him arrested. By the time it's all said and done, he's just glad to be done with the whole thing so he never has to deal with Vic Mackey and his corrupting influence ever again.
Noah Bennet (a.k.a. HRG) began as an agent of the evil Company, who hunts down those with superpowers and either captures them or kills them. Bennet quickly gained sympathy due to his genuine love for his family, especially his adopted superpowered daughter. It was also revealed that many of the people he captured were given training to keep their powers under control and offered a chance to use them to help others (in the case of Isaac and Eden), and the only superpowered people he killed were those who used their powers to hurt people. He quickly moved into Anti-Hero/borderline hero territory at the end of Season One, after he joined forces with fellow Company prison escapees Matt Parkman and Ted Sprague in order to shut down the mechanisms The Company was using to track all the people they caught and released.
Season 3 gives us Daphne Millbrook, a professional thief who works for and with other villains, but is clearly disgusted by most of them, never kills anyone herself, and is eventually revealed to have been working with Pinehearst because its leader would otherwise take away her superspeed, which is the only thing stopping her from being crippled by cerebral palsy.
For most of Season 3, there was also Sylar, who wants to be good but worries increasingly that he's irredeemable because the superpower that allows him to analyze and understand anything also giving him an unquenchable ''Hunger'' to cut superpowered people's heads open in order to learn how their powers worked. Eventually, he learned that he could copy their powers without resorting to murder and it was revealed that he could have gone on to be a nice, normal, productive member of society, had The Company (Noah Bennet in particular) not pushed his buttons so they could analyze how he was stealing powers.
And then, after they established all this, Sylar changed his mind, murdered his girlfriend, and decided to fully embrace the Total Bastard lifestyle, despite being capable of satisfying The Hunger without killing.
In all fairness, Sylar is a lot less of a villain than he used to be. In fact, in volume 4, he's had at least one "Big Damn Heroes" moment (saving Luke from the fascist agents under the employ of the psychotic bigot "Bastion" wannabe Danko), spared Luke's life on 3 separate occasions when it would have been easier to kill him, and spared the life of Luke's mother despite the fact that she was a potential witness. He's only killed so far when it was kill or be killed, or plain, old-fashioned revenge (to quote Anti Villain supreme Captain Cold).
And now he's gone back to being an unrepentant brain-eater, by joining forces with The Man, just so he can have access to a never-ending all-you-can-eat buffet of powers whenever they kill any harmless individual with a cool superpower. End of Season 4, he seems to be rehabilitated...again. Mostly because Matt Parkman trapped him in a nightmare where he was the only person in the world, which was messed up by Peter Petrelli borrowing Matt's power and following him in after he had a dream that Sylar would save Emma, a friend of his. Which...Sylar does, with a Crowning Moment of Funny when he tied up Puppeteer Doyle like...a puppet.
Holtz on Angel was a revenge-maddened vampire hunter back in the 18th century, when Angelus was racking up a body count. He only became a villain when he arrived in the 21st century because he continued to seek revenge against Angel, who was now ensouled and fighting for the good guys. Had he been willing to look past his desire for revenge and do the right thing, he could conceivably found reason to fight alongside Angel.
Mayor Wilkins. Whilst unquestionably evil (his ultimate aim seems to be to grow into a big demon and eat a few dozen teenagers), he has a genuinely fatherly love for Faith. So much so that, even when she's on the other side of the Heel-Face Revolving Door, he's still the person she remembers with the most fondness, judging by her interaction with the First.
Before becoming an Anti-Hero, Spike was this for his single appearance in Season 3. He was just too heartbroken to go all-out with the evil.
Given that Torchwood's parent show Doctor Who is a Long Runner, it's not surprising that the show has had many Anti-Villains over the course of the run. One of the most surprising came in The End of Time, when The Master, of all people, is revealed to be an Anti-Villain: he was deliberately driven mad as part of Rassilon's Xanatos Gambit. When he finds this out, he is pissed, and he gets a Heroic Sacrifice shortly thereafter.
Even more surprising one from the Time War is the War Doctor.
Sam Adama is a ruthless gangster who genuinely cares about and is fiercely protective of both his family and his culture. That Taurons are a minority on Caprica that suffers a great deal of prejudice also factors into this.
One could say that Zoe, in all her incarnations, is this, given that she willingly associates herself with monotheistic terrorists. She only wants to make the world a better place, convinced that society's grown morally directionless and soulless. Similarly, Daniel Graystone could be considered an Anti-Villain. After all, he created the cylons and is generally a fairly cold and calculated businessman. However, he has moments of softness and seems to have genuinely loved his daughter, even if he has issues relating with her or her robotic copy. Given that Caprica is set in a universe with Gray and Grey Morality, this is to be expected.
In Supernatural, Lucifer tries to come off as this, declaring that his "crime" was loving God too much. It doesn't really work, since there are three groups he can give it to: Demons, who hate God and humanity both and would probably be less in awe of him if they knew that was his motivation; Angels, who were all faced with the exact same situation and made the other choice; and Humans, who are going to be wiped out en masse by his war against heaven. In fact, the conclusion most people come to is that he's a bratty child throwing a tantrum and breaking his dad's toys.
His brother, Gabriel/The Trickster, does this much better. After it's dicovered who he is, it's easier to see why he killed Dean so many times: he was trying to stop Sam from snapping and going after Lilith after Dean dies, therefore trying to stop him from breaking the final seal. He comes across as more the little brother who can't stand his brothers' arguing, to Lucifer's bratty persona. Sadly, in Gabriel's case Redemption Equals Death and he's killed by Lucifer - but not before leaving Sam and Dean a DVD which tells them how to put Lucifer back in his box.
Jesse Pinkman from Breaking Bad. He says that he's the bad guy, yet seems to have more moral fiber than anyone else in the drug business. Walter White could qualify for this too, but by the end of season 3, he seems to be more of a Villain Protagonist.
While Scorpius of Farscape is absolutely a Magnificent Bastard, his motivation behind revealing his Freudian Excuse to John seems (at first) to be an attempt to paint himself as an Anti-Villain. While he has some villainous motives and does some truly unforgivable things, he honestly thinks he has worthwhile motives: defeating the bad guys. John (and the audience) doesn't really buy it until he actually meets said bad guys and concede that he at least has some semblance of a point.
Crais very early on enters into the anti-villain mode, and much of what he does is driven by simple revenge for the death of his brother. (That said, he still indulges in some straight-out villainous behavior, such as snapping the neck of a female subordinate.) Later in the series, he moves beyond anti-villain into Anti-Hero, if not full Heel-Face Turn territory, particularly after the birth of Talon.
Nucky Thompson, the main character of Boardwalk Empire. Yeah, he's a corrupt Sleazy Politician who started looking into becoming a kingpin of the illegal booze trade the moment Prohibition started, but he's also often a genuinely kind man with good intentions, has much more enlightened views on women and minorities than his peers, has some genuine Freudian issues going on, and seems positively cuddly when contrasted with the viciousness of Al Capone or the cold-blooded sadism of Arnold Rothstein.
Glee's Sue Sylvester occasionally edges towards this trope, as her Morality Pet moments with her sister, Jean, have been expanded into a real relationship, her positive treatment of Becky has continued, and she has genuinely attempted to help Kurt deal with both a situation that verged on religious harassment and serious bullying - to the point where she resigned her Principalship in order to be able to help him better.
Smallville: Lex Luthor evolved from an Antihero into an Antivillain in Season's 4 & 5, retaining most of his sympathetic qualities, but becoming directly antagonistic. Eventually, he lost those as well, and evolved into the Corrupt Corporate Executive and sociopath we all knew he'd eventually be. His father, Lionel, evolved the other way. Beginning the series as an unrepentant Big Bad, Lionel became an Antivillain in the later seasons, as his crush on Martha, revelations about his past, and attempts to make up for his many mistakes humanised him. Some would argue that he even managed to become an antihero (Type IV) before his Season 7 exit.
This changed in the "6:02 AM EST" episode, when Walternate revealed that he was willing to kill his son in order to save his own universe. Contrast this with our Walter, who has always been trying to find a way to save both universes.
In the same episode, Walternate also captures the mother of his grandchild and locks her in a cell when his disregard for his own son's life causes her to attempt a Heel-Face Turn.
Then there's Mags Bennet, who is a clearer Anti-Villain, committing crime, but only in the best interest of her kids and grandkids. It helps that she has a Morality Pet in the form of Loretta McCready.
Arguably, Babe Carey, from All My Children, circa 2003-2007. She never wants to do bad things and is usually, in some way, pushed into doing the wrong thing (for the right reasons) because of the effects of others' actions. She doesn't want to be bad and, in ideal circumstances, she would even be good. She strives and wants to be good. However, she is not strong enough to rise against her circumstances.
Khan Noonien Singh in his appearance in the episode "Space Seed" of Star Trek. Although fandom (and some of the writers of the later series) have made him out to be a complete monster, it's stated that he was the only good dictator in the Eugenics Wars. He was neither bloodthirsty nor a warmonger, and rather than assume a scorched earth strategy when he was defeated, he took his people and fled into space to find a new world. In fact, in "Space Seed" he doesn't even kill anyone (though he does come close in the case of Kirk and at the end, he is actually quite happy with Kirk's suggestion of leaving him and his crew on Ceti Alpha V, since he and his people will finally have what they wanted: a world to themselves. It was only after spending twenty years on a dead rock that he became the monster we saw in The Wrath of Khan.
Rodrigo Borgia genuinely wants to strengthen Rome as pope. He even takes an interest in alleviating poverty in the second season, and has always loved his family, perhaps to a fault. He also, however, blackmails/tricks virtually everyone he works with, orders a few assassinations, and is quite the lech. Like most Renaissance-era fathers, he also has very little regard for his daughter's freedom and will marry her off to whoever he wants, though he is trying to make sure she doesn't get a bad husband... this time around. Overall, he's still one of the least villainous members of his family.
His son, Cesare, was at first a sort of anti-villain—the majority of what he did was for the good of the family. However, he really didn't have much pity for anyone beyond his family, and remained ruthless, cynical, and fairly cold-blooded. Nowadays, he's in solidly Villain Protagonist territory. What with murdering his brother and all.
JAG: Colonel Matthew O’Hara is a Marine Corps legend who earned the Medal of Honor in the Vietnam War, but he’s grown tired of American degradation of society with street crimes and corrupted politicians, so he and a few other Marines snatches the Declaration of Independence transported in a mail truck on its back from a restoration job. What no one knows at the outset is that the Colonel is the uncle of Major Sarah Mackenzie.
One of the memorable twists in the final season of 24 was having Jack Bauer himself become one in the final episodes of the series. Although he has a mostly noble goal in mind ( exposing the conspiracy regarding a foreign President's murder that current U.S. President Allison Taylor is covering up after undergoing a Face-Heel Turn), they are tainted by the desire for revenge after he finally gets screwed over for the last time, leading him to pull some pretty terrible acts even for him that not only cross the line, they double over it.
While the Kamen Rider franchise is not know for providing the most nuanced interpretations for its villains, they do occasionally appear, especially in the Heisei era of the franchise. Although to date, the only series in the franchise that had the Big Bad as an Anti-Villain, is Kamen Rider Ryuki where Shiro Kanzaki's motives are sympathetic enough that much of what he does in the series is understandable, if not condonable.
Scandal: Cyrus, possibly. It's still not clear what his motivations are.
Firefly: Had Harken, an alliance commander who arrested the whole team after finding them stealing from a damaged ship. He spent much of the episode grilling them, while searching the ship, and he has them detained after his men find a brutally mutilated survivor and he assumes the team had done it. When the survivor escapes and goes on a killing spree, his first order? Reinforce security at the nursery, and then he leads a team, and Mal, to stop the man when he gets back on Serenity. At the end, after Mal saves him, he releases the crew and drops the charges, though he does confiscate all the stuff they stole, because it was Alliance property.
Alex Russo on Wizards of Waverly Place. She is self-centered, manipulative, irresponsible, and often cruel to those she loves, but she really does love them and will usually do the right thing in the end, even though "the right thing" usually means fixing a problem she created.
Enos from Dukes Of Hazzard is only really a villain by virtue of being an upstanding deputy sheriff and on the side of the Law, and thus antagonistic to our less law-abiding heroes. While he is willing to stand behind most of his corrupt boss' schemes, he is too righteous to be a part of them. He is the one lawman the Dukes have any respect for, and they have said as much in public.
Jason Winkler from the first season of House of Anubis. He was only really a villain by way of being a member of the Secret Society and betraying Patricia. He was always more interested in his teaching job and the students, and even after betraying Patricia, still clearly cared about her. In the finale, he attempted to get Victor and the other teachers to help Sibuna, who were trapped with Rufus Zeno. It was then revealed that the only reason he joined the Society at all was because the elixir of life, which makes one immortal, would have saved him from dying of his degenerative illness. In a deleted scene, he even got to talk to Patricia one last time before disappearing from the show. He was never at all a bad guy, he had just made the wrong choices.
Kiera Cameron from Continuum is a type III, anti-villain protagonist fighting a group of type IV and V anti-heroes. Initially she is depicted as a "good" police officer from 2077 idealistically opposing the terrorist organization Liber8. It quickly becomes clear that the future society in which she lives is a high surveillance corporate police state and the terrorists she is fighting against are freedom fighters who are trying to tear down the police state and bring back democracy, human rights, corporate accountability, etc. Kiera's primary goal is to stop Liber8, protect the future that she knows, and get back to her family, even though this means occasionally using very brutal tactics and ultimately protecting the police state that has enslaved most of humanity. Despite all of this she cares about protecting the people and puts her own future at risk in trying to stop the deaths of thousands of innocent victims. The audience can sympathize with her as the protagonist because she idealistically believes that the future she is trying to protect is truly the best option for humanity and she doesn't recognize herself as a villain (the extreme violence of Liber8 also makes it easier to sympathize with Kiera as a protector of the people). This is lampshaded in "Second Time" when Travis says to her, "When are you going to wake up? You're the villain in this tale."