The Junkman in Astro City. He was a brilliant inventor who was removed from his job only because of the company's mandatory retirement policy; they wanted him to relax and enjoy his twilight years, but he simply wanted to keep working. The only reason he turns to crime is to show society that discarded things can still have value, and builds his arsenal out of junk just to prove his point. It's not hard to imagine that he could be a happy law-abiding citizen if someone would just give him another job.
Laszlo Herzl in the Blacksad album Red Soul is shown first as someone full of spite towards Blacksad's one-time mentor Otto Lieber, and later is responsible for the death of another scientist. However, there's more to it than that: Lieber is a former Nazi scientist, and Herzl is a Holocaust survivor who's furious that a Nazi is getting away unscathed thanks to being recruited for Operation Paperclip - especially since he's also aware Lieber is selling secrets to the Russians. Blacksad ultimately admits that Herzl has the moral high ground and confronts Lieber instead.
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 Heel–Face 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.
Sin City: Nearly every villain in the franchise is motivated by nothing but For the Evulz or pure Greed. Most of them are utterly devoid of likable qualities. Even comical villains like Klump, Schlubb, and Gordo are involved in some pretty nasty stuff like aiding a pedophile and human trafficking. This makes the only four antagonists who actually do have some better traits stand out quite a bit (particularly the former two).
Liebowitz. He's as corrupt of a cop as any other and beats up Hartigan for not signing a false confession. Despite this, he is a devoted family man and eventually turns on the Colonel, going so far as to kill him. In the second film, Liebowitz goes out of his way to warn Johnny to leave the city after he beats Roark in a poker game.
Don Giacco Magliozzi is a downplayed example. He's a fairly unpleasant mob boss, but he deeply loved his niece Andrea and values avenging her death over continuing a profitable partnership with her Hate Sink killer's employer. If he hadn't entrusted the hit to his Trigger-Happy nephews, who accidentally kill an Old Town prostitute, then he'd barely count as a villain at all.
Dirty Cop Bob covers up the crimes of pedophile and Serial Killer Roark Jr. and shoots his own partner. However, he claims that he's only doing so out of fear that the Roarks will kill him, and tries to convince Hartigan to lay down his gun for several seconds before shooting him again. In A Dame to Kill For, he's quick to believe that Dwight was set up and shows concern for his new partner.
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.
