- Brennus: The Dark, the original super-villain, qualifies due to being a) a Noble Demon whose organization helps keep the hero-villain conflict from escalating to truly uncontrollable levels, b) being in Enemy Mine situations with the heroes more often than he is in conflict with them, and c) a genuinely loving father and Benevolent Boss. At times he comes off more like a full on Anti-Hero, but remember that he still willingly employs cannibals and Serial Rapists, and he's the one who gives them their marching orders, and he has no small amount of blood on his own hands.
- Most of oWn in Cult of Personality are no less moral than other characters in RED and BLU, mostly because the mercenaries who joined oWn have their personalities largely intact despite their changed loyalties.
- The Gear Group during the Keep the Flag Flying arc in Our Avatars Were In A Room Together The Continuation, if only because they're slightly sympathetic in their motives, which is to get revenge on the humans that experimented on them.
- Tenshirock from Noob is a villain mostly due to most character being gamers while his objective is getting people to stop playing MMORPG. He's otherwise partners in crime with the Manipulative Bastard among the protagonists and Friendly Enemies with the rest to the point of You Will Be Spared.
- Fallout Is Dragons has Death, leader of one quarter of the Four Horses Raider Gang. His status as villain is mostly given by his position; in person he's actually quite reasonable, acts as an unofficial mentor to one of the player characters, and is willing to stop the raids on towns if it will help his gang.
- In commentaries, Doug said he wrote The Nostalgia Critic and company in Kickassia and Suburban Knights this way; selfish and doing bad things, but sympathetic and at least in the end knowing what's right. By To Boldly Flee, Critic's broken enough to just want to be the hero, and succeeds, while everyone else is nicer too.
- The main characters are a group of supervillains called the Undersiders, whom on some level have at least a little anti-villain flavoring (with the possible exception of Regent). Taylor becomes a supervillain because she couldn't betray her friends in addition to Jerkass superheroes, and constantly tries to minimize the harm her actions do and keep innocents from getting hurt. Tattletale becomes Taylor's friend to stop her from committing suicide by villain or whatever fresh horror just arrived in Brockton Bay. Brian became a Punch-Clock Villain to take care of his little sister Aisha. Bitch is a antisocial thug who due to a harsh, abusive upbringing doesn't trust any other humans anymore, but genuinely loves dogs and provides funds for the shelter she starts running for them. They also serve as A Lighter Shade of Black, being a thieves' gang who find themselves pitted against threats like white supremacists, criminal masterminds trying to take control of the city, and wandering bands of hero killers, and do a better job of fighting them than the heroes.
- Arguably, the leaders of Cauldron. They're utterly ruthless, but everything they do is directed toward the goal of saving as much of the human race as possible from Scion's inevitable FaceHeel Turn into a nigh-omnipotent Omnicidal Maniac. Also, they know for certain that their means are necessary to achieve that end because of Contessa's power, which is basically Combat Clairvoyance turned up to the level of a Story-Breaker Power — it doesn't just let her see a path to victory in a single fight, she can project the path to victory in a decades-long global conflict affecting hundreds of parallel Earths.
- Dr. Horrible's Sing-Along Blog: Dr. Horrible. He claims to be a Well-Intentioned Extremist but is really an Ineffectual Sympathetic Villain who's in the whole evil business because of constant humiliations from Jerk Jock superheroes like Captain Hammer and unrequited affection for a girl he met at the laundromat. The story follows his transition from Anti-Villain to full-blown Supervillain. In "Fury of Solace", originally created for the ELE application contest note , his Villain Song details how he had to kill a young girl's parents (and, implied by extension, become her nemesis) so she'll become a superhero and save the world. One of the prequel comics show that Penny actually likes him too.
- Despite going criminally insane and burning down a toy factory in a rampaging fit of revenge, Doctor Steel is really a kind-hearted soul who only wants to make the world a better place (for himself...).
- Vincent Liedecker of The Descendants, philanthropist, life saver, and sponsor the hero team's school — the only one around that doesn't seem to be about brainwashing or supersoldier projects. He sends his thugs to protect the establishments he takes protection money from, even from threats that he didn't create or provide the weapons for. Er...so he is into protection rackets and the underground economy, and producing Magitek and cloning horrible monsters that Should Not Be, and then selling them to the highest bidder...
- In the Practical Guide to Evil, this is Catherine's explicit aim, and part of Black Knight's plan seems to be to create such a role for Evil names. Likewise, Thief also fills this role, joining Catherine because she'd be better joining her.
- In Survival of the Fittest, the closest things to villains per se are those who choose to play the game. While sometimes these people are downright evil or simply terrifyingly insane, there are killers who actually aren't very bad people, often given a sympathetic reason for playing the game such as trying to protect a loved one or because they've given up all hope of escape and see it as the only way to survive (and as far as they know, it is). Examples of this include Bobby Jacks,
Lenny Priestly(not... anymore), Bryan Calvert, to an extent, and, arguably, Jacob Starr.
- Dudley Griffin in KateModern was fighting the Order long before the heroes, and tries desperately to warn Kate away from danger. Nevertheless, with his willingness to attack other good characters and his bad temper, he functions as an antagonist.
- The Global Guardians PBEM Universe features the supervillainess Embrace, a super-terrorist who tends to target inhuman Third World dictatorial regimes and the First World nations who prop them up while simultaneously protecting the innocent peasants who are those regimes' primary victims.
- There are plenty in the Whateley Universe. Dr. Diabolik is responsible for the deaths of thousands, all in his campaign to improve the human race. Brigand is a wanted supervillain who is actually trying to track down the monsters who corrupted his father. Jobe Wilkins is a Heroic Comedic Sociopath who thinks nothing of testing serums on unwilling criminals if it provides a new cure for dysentery.
- Even some of the more antagonistic characters have shades of Anti-Villain. The MCO, for example, is filled with a number of people who genuinely do believe that they're protecting humanity, even if it has its share of genuinely mutophobic... let's say 'jerkfaces'. The Syndicate, probably the closest thing to a 'League of Supervillains' that the Whateley Universe has, is actively involved in trying to prevent worse things from happening... like Dr. Palm's, or the Bastard's, goals succeeding.
- Some Imperials from The Gungan Council, like Akio Kahoshi and Delek Wrentar, usually want to bring peace to a war ridden galaxy and care for their close friends. Yet, their methods to bringing peace usually involve hostile conquests of systems and purging the Jedi.
- In The Gamer's Alliance, Kagetsu I deeply cares for his subordinates and loves his wife Marya above anything else. He knows that his plan of destroying the world, killing countless innocents and depowering the gods is an unfortunate but necessary step to create an everlasting utopia but he hesitates when he has to choose whether to sacrifice Marya to make his dream come true. Glaurung shares a vision of a world without borders where no more warfare is necessary, but in order to do so her armies have to crush any opposition.
Antivillain / Web Original