100 Bullets: While The Trust are an ancient conspiracy controlling America behind the scenes many of them just seem to be along from the ride (due to the hereditary nature of the organization) and are being manipulated by Augustus and ruthlessly hunted down and killed by the Minutemen. It's implied that a few of the oldest members and the fathers/grandfathers of the rest had Kennedy killed but the worst thing some of the present generation do is simply try to get rid of their hired assassins in an effort to become less violent and law-breaking.
Ocean Master, Aquaman's evil brother and Arch-Enemy was made into one of these in the New 52. Typically portrayed as a usurper and Evil Sorceror who sold his soul to the devil, post-Flashpoint he was repackaged as a Noble Demon and warrior king who ruled Atlantis fairly well, actually seemed to genuinely love his brother, and whose most villainous actions were the result of him being manipulated by outside forces. He isn't a good person by any means, he's an Atlantean supremacist and smirking, arrogant prick, and hell kill anyone who gets in his way, but you could make the case that he was often doing what he believed was right. Aquaman admits that when he first came to Atlantis, Orm welcomed him with open arms and happily abdicated, and only took the throne again when the people demanded it. When he is imprisoned on land for his part in Atlantis' attack on Boston, after he joined forces with Arthur against Vulko and believed they had mended fences, you almost feel sorry for him.
When Aquaman's friends start being attacked and killed for their Atlantean relics, Arthur and Orm secretly meet in a shipwreck deep under the sea. Arthur asks Orm if he is behind it, and Orm replies that if he wanted the relics he would just ask Arthur for them, and says he would never lie to his brother, which Aquaman doesn't contradict.
During the Forever Evil event, during the mass escape from Blackgate Prison, while all the other inmates go crazy attacking the surrounding areas, Orm just walks to the shore hoping to go home, and abandons that to save a single mother and her son from a gang of escaped supervillains.
Recently, he has repackaged himself as a champion of the downtrodden, creating a new underwater city as a refuge for Atlantis underclass of homeless, mutants and outcasts, as well as handing out free food and medicine to the poor while railing against the failings of the Atlantean government. Its a nakedly cynical rabble rousing to undermine his enemies and anyone who comes to him for help has to pledge unthinking fealty, but at the same time, hes A. fairly accurate in his assessment of Atlantean society and governance, which is horribly unequal and has a lot of significant structural problems and generally only functions well if a forceful, charismatic leader like him, Arthur or Mera is running the show, and is stubbornly resistant to any change or progress (Mera is shown having to browbeat her own ministers into carrying out social welfare projects to improve the lives of Atlantis poorest citizens); B. he genuinely cares about the assorted social refuse flocking to his banner; and C. regardless of motives, hes the only one offering much-needed humanitarian aid.
In an old The Atom comic, the title character encountered the 2-D Man, able to shrink on his horizontal axes, but not his vertical. Slowly shrinking on that axis, "dwindling away to nothing," in his own words, he stole the high-tech equipment he needed to save his life, and continue his research into a leukemia cure, using another product of the same accident that gave him his powers. When he's cured of his shrinking problem, the judge essentially gives him probation so long as he actually works on this cure.
A vast majority of Batman's Rogues Gallery regulars are anti-villains of some kind. Examples include:
Clayface, a former actor who just wants to be normal again (although some of his counterparts are egotistical assholes who deliberately turned themselves into monsters).
Mr. Freeze. Victor Fries was a scientist and a doctor whose wife, Nora, had a terminal disease. He put her in cryogenic stasis until a cure could be developed, but an "accident" that followed turned him into a mutant that can only survive at sub-zero temperatures. Afterwards, he dedicated himself to trying to find a way to save Nora and take his revenge on the people who ruined his life (until New 52 that is, where he was turned into a crazy man who just imagined his marriage... up until DC Rebirth came along, making Nora his wife once more).
The original version of Two-Face was portrayed this way. Because he would only commit crimes when his coin landed scarred-side up, he was only evil half the time, and when the coin landed face-up he would do good deeds. His portrayal gradually shifted away from this to Black-and-Gray Morality, where his "good side" merely became "less evil" and cowered under his dominant evil personality.
Poison Ivy can be this from time to time, Depending on the Writer. She would gladly wipe every human being from the face of the earth to protect the natural world, but has had a number of significant Pet the Dog moments. In particular, she has a soft spot for children and Harley Quinn. When she and Harley team up, she acts as her Cool Big Sis (and maybe more, again Depending on the Writer), and seeks to end her self destructive relationship with the Joker. As for the children, when the quake devastated Gotham, she took up residence in Robinson Park and adopted sixteen children who had been orphaned by the disaster. She cared for them like a mother, and made a deal with Batman to grow food for the people of Gotham if he would let them be. After the city was rebuilt, the cops tried to evict her with a defoliant, and she was prepared to martyr herself for the park. But when one of the children was hurt she surrendered peacefully to get her medical aid. Even Batman acknowledges that deep down Ivy's still more human than plant.
Catwoman is an interesting example, in that a lot of the time she's an unapologetic jewel thief, but when push comes to shove she'll usually help Batman and do the right thing. The fact that she's one of the few Batman villains whose various plans usually do not end with lots of people dead or critically injured probably helps as well.
Killer Croc in the Post-Flashpoint universe is this in spades, especially when written by Tim Seeley. He protects Gotham's cast-aside and disenfranchised in his own personal underground sewer kingdom, will fight magical monsters from another dimension if just one of them is endangered, sponsors Roy Harper for alcoholics anonymous, hunts down corrupt cops when he sees them kill somebody who was nice to him, and joins up with Catwoman when she becomes Gotham's criminal kingpin, recognizing her as the lesser of all evils in the city.
Black Adam, traditionally seen as the bad guy to Captain Marvel's position of hero, made big changes under Geoff Johns. He led a team of anti-heroes including Atom Smasher and an at the time reformed Eclipso to overthrow a dictator of Adam's ancestral home. Adam made himself the dictator, but used his super powers to enforce a system of even handed justice, personally executing super criminals to the cheers of millions; he also created treaties with China and Russia during 52 to further his nation's place in the world; built a ton of infrastructure, freed slaves, and battled organized crime; and created his own team of side kicks, his wife Isis and brother-in-law Osiris... Then Osiris and Isis got murdered. Black Adam massacred a middle eastern country in a battle with a Cyborg Angel of Death and then tried to wipe China off the map and ended up in a fight with everybody.
La Dama, a female crime lord and supposed nemesis of Blue Beetle. She's happy to stay a more or less regional mob boss, but at the start of the series is trying to gain a bit of control over the magic and metahuman communities as well. She figures out Blue Beetle's secret identity at the same time as he figures out that she is the aunt of his best friend Brenda, custodial after the suspicious death of her father. So they actually keep each other's secrets for a while. Throughout the series she's a mob boss, although any actual illegal activities fall out of the picture eventually, but she was never seen as all that bad to begin with and has definitely given Brenda a healthier home life than she had before.
Geoff Johns has been working to turn former alien despot Sinestro into this. Formerly a rather one-dimensional villain obsessed with power and revenge, his Post-Crisis origin gave him a bit of humanity, so to speak, suggesting that he was the ruler of his planet out of necessity rather than choice. Then Geoff got hold of him, gave him a dash of Well-Intentioned Extremist and a few gentle retcons, and now he's barely recognizable from his first appearances.
It's worked so well that when Sinestro appears in the animated Emerald Knights, set sometime before his FaceHeel Turn (which is hinted at during the story about Abin Sur), he is seen as a heroic and noble figure without any problem at all.
Atrocitus is another one. You'd assume the leader of the Red Lantern Corps and the embodiment of Rage would be as clearcut a villain as you'd get: you'd be wrong. This is mainly because what the rage-powered Red Lanterns are, well, raging against is injustice—every Red Lantern was wronged greatly in some way, and harbored great rage and resentment over it. The Red Lantern rings are noted as taking the place of their bearer's hearts—they give themselves over to it, though Atrocitus seems to have his own rage mostly under control.
Earth-10's Overman from Mastermen #1. He feels immense guilt for the lives lost in the creation of his psuedo-utopia, to the point of becoming The Mole for the Freedom Fighters.
Many of the Secret Six in the comic book of that name—it may be the entire point of the title. In particular, Catman often displays noble qualities—Deadshot, Scandal Savage, and Bane to a much lesser extent. Ragdoll is pretty-much outright evil by comparison, but affable in his way.
Shade shifts from Anti-Villain to Anti-Hero as it suits him. He protects Opal City to an extent and has a soft spot for kids but is largely disinterested in the fate of everywhere else and sometime picks fights with The Flash or the entire Justice League of America out of boredom. That one time he tried to destroy the world has been retconned to not have been his fault, which makes sense as it would have been really difficult to stop him if he'd really wanted to.
Superman enters this territory in Superman: Red Son. As a leader of the USSR, he is a huge threat to the US and ends up ruling huge portions of the world population. But he still retains most of his heroic qualities, is attempting to create a utopia, and is very reluctant to actually do wrong. This is opposed to Lex Luthor, an Anti-Hero who is America's only hope, but also a Machiavellian egotist; he doesn't actually care what happens to America, just as long as he can get one over on Superman.
Some depictions of Lex Luthor have portrayed him as an anti-villain whose sin is an excess desire to keep the Earth safe from alien invasion coupled with excess pride. It's fairly common now to find Lex and Superman finding common ground and working together, especially in non-canonical stories.
Demon Spawn: Technically Nightflame wants to save her world and its denizens... by destroying Supergirl's soul, taking over her body and doing evil things.
In Supergirl (Rebirth), Zor-El only wants to save his family and his city. In order to accomplish this goal, though, he makes choices which are morally dubious at best (such like sending an innocent man to an eternity of ghostly imprisonment because he was potentially dangerous), and his sanity decreases with each failure.
Even Ares can fall here, since he's a product of what he is and can never truly reform. Once Diana shows him the full truth of his plot to start WWIII and he immediately calls it off and melts the humans who'd invoked him. Afterwards he will aid her on occasion and definitely does not want the destruction of the human race but he's treacherous and slippery at the best of times and it's been established that too much power drives the Olympians mad, and he's got plenty streaming in.
Circe. After her stint as Donna Milton she can't forget the true friendship she and Diana once shared, and while she hates that she can no longer be what she was or Donna Milton ever again and still viciously attacks Di she'll also go out of her way to save her and absolutely adores and loves the daughter she had during this period. Many of her attacks after this are attempts to get her daughter back as she was taken in to be raised and protected by the Amazons.
Giganta transferred her consciousness to an innocent woman killing her in the process in order to save her own life from a painful terminal illness. She can't return to civilian life as a known murderer and she refuses to cooperate with the justice system so she's a Punch-Clock Villain. It helps that the new body came with superpowers.
Silver Swan III was a huge fan of Wonder Woman and had long been her friend before being kidnapped, tortured, experimented on and Mind Raped via magic and telepathy into becoming a villain. She was saved by Wonder Woman who was able to find doctors who could remove her "augmentations" and went on to graduate college and lead a normal life.
Hypnota turned to using her newfound powers for theft because she developed them after the person she trusted the most in life, her twin sister, shot her in the head. It was an accident but Hypnota thought she'd tried to kill her and it broke her ability to trust. The later revelation that she'd also become a human trafiker makes her considerably less sympathetic, but it's noted that the physical brain damage of getting shot in the head has altered her personality.
Pre-Crisis Paula von Gunther only worked for the Nazis because they were holding her daughter Gerta hostage. Once the girl was rescued, Paula defected to Paradise Island with Gerta in tow.
Silver Swan II's entire motivation was her desire to be loved, and she was taken advantage of and abused by those running a meta-human experiment which worked on her, adding metal augmentations as well. After she was made to see the truth of her situation she left those driving her to attack Wondy and after helping fight against Circe once retired to a normal life.
Zara's hatred towards humanity was born from being sold into slavery as a child.
The Mock Turtle in Astro City has it all - frequently insulted by others, repeatedly denied the opportunity to be special, stealing from the rich in order to support a poor neighbourhood and not, as far as we know, ever actually killing anyone.
Ozymandias in Watchmen who had a plan for saving the world, by killing half the population of New York.
In the movie version, he upgrades it to killing half the population of ALL the world's major cities, and removing the most effective nuclear deterrent.
While he does physically remove the most effective nuclear deterrent, in practice he validates Manhattan's status as a nuclear deterrent, that's the whole point of his plan, making sure the world knows that he'll actually do something about it.
Adam Susan of V for Vendetta. He's a Fascist dictator whose regime has killed countless people. However, he sincerely believes in Fascism and has some moments (particularly towards the end) that make him into an absolute Jerkass Woobie.
Armadillo is a minor enemy, but Cap has never regarded him as anything but a confused individual, a good man who keeps making poor decisions with his life. Having fairly low intelligence and little personal initiative, he's easily manipulated by smarter people. Stuck in a monstrous body, his ultimate goal has always been simply to find a cure for his condition, and he has acted heroically on several occasions. Cap has hope that one day he'll see he's a better man than he thinks he is. He even recommends that Armadillo receive guidance counseling rather than prison time in his official evaluation!
Cap profiles dozens of villains in Heroic Age: Villains, and considers a number of them to be victims of circumstance or misunderstood rather than evil. The Bison, for instance, is a young man who cut a raw deal that turned him into, well, a bison man. He only hires out his services as a villain because he can't get work any other way and he wants to provide for his girlfriend.
Doctor Doom, arch enemy of the Fantastic Four, has been known to defend his actions on this basis from time to time, especially in regards to his iron-fisted rule over his small Eastern European homeland Latveria. Considering Doom showed the Four the apocalyptic mess that the insane Prince Zorba made of the land after he took the throne, the Four were forced to agree that Doom would be preferable and help him retake the throne after Zorba orders a murderous purge of the population to thwart his predecessor. The Four would have been more than willing to immediately take down Doom afterward if he hadn't installed mental inhibitors in them to force them to leave instead.
Dr. Doom has some despicable moments that subvert this trope, mainly selling the soul of the only woman he loved to demons in order to gain mystic power and send the Richards children to hell. But depictions on Doom and what Doom should be like is a matter writers can't seem to agree on, and various people at Marvel make a point to declare stories about Doom they don't like as having not really been him, or simply file them under Canon Discontinuity. Even his aforementioned rule of Latveria can go from a beloved kingship with happy citizens to a fearful populace run by an egotistical dictator. In other words- he's sometimes an Anti-Villain. It depends on the writer.
Similarly, Dr. Doom turns out to be the only world leader in Marvel Zombies who actually managed to save his people from the zombies (by sending each of them to alternate worlds of their choosing via a jury-rigged dimensional portal), while staying behind to fight off the attacking zombie heroes and then, after being infected, destroying the machine so that even he can't go after his subjects once he's turned. He does this in part by using the weak and elderly as zombie bait, though.
Magneto suffered a very similar fate in the same overall storyline, although he did so without being as coldly darwinistic as Doom (though it's implied that his only concern, at least at first, was saving mutants.)
Magneto of X-Men fame is a Holocaust survivor who has taken "Never Again" to its extreme conclusion. A Well-Intentioned Extremist who has frequently shown kindness and mercy towards his rivals, most of his victims tend to deserve it, such as the angry mob responsible for the death of his family. He has done more than one HeelFace Turn, and has a deep respect for arch-rival Charles Xavier.
Actually it's in-canon that Magneto had his truly villainous moments (he once tried to nuke New York For the Evulz) but they're attributed to madness from his tragic life events (Depending on the Writer; sometimes he is written as just an extremely high-functioning Sociopath who cares more about mutants as an abstract ideal than he does any actual flesh-and-blood mutant). After being artificially de-aged into a baby (and then later aged back to an adult) he was cured of it. And then relapsed (and was cured again, and relapsed again, because Status Quo Is God in comic books).
Presenting an interesting contrast to Magneto is his sometimes-Dragon, Exodus. Their goals (defending mutantkind and/or mutant supremacy) are virtually identical, so too are their methods, but while Magneto is a Mastermind type of leader who assembles and maneuvers his team with cold pragmatism, Exodus tends to be the Headstrong type of leader who is always at the forefront of every battle he leads a team into. Both characters have Charismatic leadership as a subtype, so rarely do either of them lack for followers.
Namor goes between this and Anti-Hero, sometimes in the same book. Sometimes in the same panel. Most (if not all) of the villain side comes from his loyalty to Atlantis above all.
Perhaps best summed up by his belonging to a super-secret group of good guys (the Illuminati) and a super-secret group of bad guys (Norman Osborn's inner circle) at the same time. And apparently not seeing the need to tell either group about the other. It's even been implied that at least once, he left a meeting with one group and went immediately to a meeting of the other group. Talk about blurring the lines!
Who else but Namor can claim to be best pals with both Captain America and Dr Doom.
Axeman Bone in Skaar, Son of Hulk. He may be a brutal warrior but, as he makes a point of expressing, at least he knows what he's doing (trying to unite his people and re-establish formal society on Sakaar) and when to stop, unlike the aimless and animalistic Skaar.
The Sleepwalker villain Spectra is first seen planning to steal a valuable synthetic diamond and sell it for drug money, until the diamond becomes involved in a Freak Lab Accident that imbues her with its light-based energies and gives her superpowers. While she initially seems poised to become a supervillain, she has apparently had a change of heart by the time Sleepwalker runs into her again, having taken to using her light-projecting powers to make an honest living, and only intervening to stop Sleepwalker when she thought he was a villain. Once the misunderstanding was sorted out, Spectra later helped Sleepwalker defeat the Ax-Crazy Psyko.
Puma serves in many ways as a Punch-Clock Villain, only killing people he's hired to murder as a paid assassin. He originally crosses paths with Spidey after a mob boss hires him to murder the wall-crawler, but later on comes to Spider-Man's aid on several occasions. He only kills people he's paid to, and otherwise functions as a perfectly legitimate businessman in his day job, his major concerns being his own personal welfare and the needs of his people.
Mr. Negative is a ruthless crime lord who runs drugs, weapons, prostitutes, illegal immigrants, protection... His alter ego, Martin Li, is a saintly billionaire who has dedicated his life to charitable pursuits. He feels this is necessary for the sake of balance - if a man who does great evil doesn't also do great good, his spirit will never know peace.
The Ultimates: Most of the Liberators are utter bastards, but the Colonel, at least, seems to be a genuinely good guy who just happens to be fighting for the wrong side. Indeed, his death scene is probably the most respectful send-off anyone's ever gotten in the entire series.
X-Men: Magneto's not the only anti-villain associated with the team:
Claudine Renko, AKA Ms. Sinister. Her actions are motivated purely by self-preservation: She was one of the many hapless victims of Mr. Sinister's experiments. In her case, she was infected with a virus that in the aftermath of his death during Messiah Complex has been slowly turningherintohim. She's terrified of what it will mean for her if Sinister's consciousness is able to fully supplant hers, and is seeking a new body to transfer her own consciousness into to escape what is likely to be certain death. It only gets worse after an encounter with Daken goes very badly for her, as he injures her in a manner that leaves her severely weakened. She picks X-23 to steal her body because of her powerful Healing Factor. She's never actively malicious about it, she's just desperate to survive.
Two Edge in ElfQuest. He's a Manipulative Bastard who plays a generations long Xanatos Gambit to set two races at war but he has a Freudian Excuse He was tortured into insanity by his mother after watching her kill his father and has a soft spot for children (boy children anyway and no, not in that way.) Ultimately he does a HeelFace Turn to become an Anti-Hero
While Mr. Gone cheerfully murders people and inflicts incredible anguish on The Maxx and his friends, his stated intention is to instigate Julie's emotional catharsis and to set things right with his daughter, Sara.
Bohr, the troll captain in Sojourn. He is the leader of the pursuing trolls, yet he is not fond of unnecessary violence, is loyal and determined, and loves his family.
In the Sonic X comic book, Dr. Eggman is presented as a genuinely good person who, aside from really wanting to rule the world, has a strong sense of morals and is willing to do the right thing most of the time.
Star Wars: Luke Skywalker's childhood friend Janek Sunber, aka Tank, joined the Empire and became a junior officer among its ground forces. He served with distinction and never placed himself above his soldiers, feeling responsible for their lives, and shared in menial labor that his fellow officers felt was beneath their rank. Through his natural talent as a leader and strategist, a scant handful of men survived what otherwise would have been a complete annihilation at the hands of enemy forces. Yet in the end, he was still an Imperial and conducted missions against Rebel forces, even infiltrating the Rebellion in an attempt to capture Luke and bring him to Darth Vader.
Circuit Breaker in the MarvelTransformers Generation 1 comic. She hates all robots equally, regardless of faction, but given her origin, that's understandable. Megatron also tends to feign cooperation with the Autobots purely to make people think the Autobots are also evil, furthering Circuit Breaker's hatred. Also, she is shown to genuinely want to protect other humans, repeatedly risking her own life and being severely damaged to save an innocent bystander.
Thundercracker in Transformers Ongoing is tired of the war and doesn't want to fight but still considers himself a Decepticon, he does occasionally help the Autobots in several occasions.