A vast majority of Batman's Rogues Gallery regulars is an anti-villain of some kind. Examples include:
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.
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 who's various plans usually do not end with lots of people dead or critically injured probably helps as well.
Magneto of X-Men fame is a Holocaust survivor who has taken "Never Again" literally. 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 Heel Face Turn, and has a deep respect for arch-rival Charles Xavier. Most of his more murderous portrayals have been chalked up to Canon Dis Continuity.
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. After being artificially de-aged into a baby (and then later aged back to an adult) he was cured of it.
Dr. 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 Dis Continuity. 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, so even that Crowning Moment of Awesome's grimly subverted by the means.
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.)
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 over throw 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.
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.
The Spider-Man character 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.
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.
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.
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.
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. In the other comic by Archie, on the other hand, he's the exact opposite, as a ruthless tyrant.
Two Edge in Elf Quest. He's a Manipulative Bastard who plays a generations long Xanatos Gambit to set two races at war but he has a Freudian ExcuseHe 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 Heel Face Turn to an Anti-Hero
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.
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.
In an old 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.
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 Face Heel 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.
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.
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 Woobie.
Armadillo is a minor enemy of Captain America, 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.
Spider-Man enemy 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.
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.
Thundercracker in Transformers Ongoing who is tired of the war but still considers himself a Decepticon, he does occasionally help the Autobots from time to time.