* Arguably, Max Powers of ''PvP'', although it's tough to pin down if he's a villain at all, or if Cole and Brent just take their frustrations out on him.
** WordOfGod has it that Max is not a villain and never was; he is simply a NiceGuy (though a successful one). Only in the deranged protagonistsí minds is he evil.
*** In his very earliest appearances, he was a pranking JerkAss who didn't seem to realize that the PVP crew didn't think he was funny, but [[CharacterizationMarchesOn Characterization has marched on]] since then.
* Fuchsia in {{Sinfest}} has been undergoing massive CharacterDevelopment from ChaoticEvil HornyDevil to ChaoticNeutral NobleDemon post Criminy influence.
* Baron Klaus Wulfenbach from ''Webcomic/GirlGenius''. He doesn't want to rule most of Europe with an iron fist (in fact, he hates his job and wishes he could retire to his lab), but his empire is the only check against [[ScienceRelatedMemeticDisorder mad science]]-induced anarchy. If not for his [[PsychoForHire employees]] and his willingness to experiment on Othar Tryggvassen (GentlemanAdventurer!)'s brain, he wouldn't even be a recognizable villain.
** Even the "recognizable villain" bit can be debated, given that Othar is a homicidal genius, and Klaus's experiments were specifically about the nature of mad scientist-hood and how it might possibly be cured -- and Klaus ''let'' Othar escape after threatening him. As with all characters of sufficient complexity, the villain-hood of Klaus is questionable, and all depends on what you believe is more important: a sort of forced world peace or people's right to be all that they can be.
** Agatha has realized she MAY be a villain protagonist right about [[http://www.girlgeniusonline.com/comic.php?date=20090504 here]].
* The protagonists of ''{{Narbonic}}'' are prone to attempted (and sometimes succeed) murder on each other at a moment's notice.
* The cast of ''TheLastDaysOfFoxhound'', excepting [[MagnificentBastard Ocelot]] and [[SociopathicHero Mantis]], are partially or wholly anti-villainous. Raven would never be counted as a villain by anyone aside from his involvement with the group when it goes rogue, Wolf is at worst a PunchClockVillain and a genuinely decent human being away from her job, Octopus is often a bit slow on the draw but a laid back prankster who has never killed anyone, and while [[IdiotHero Liquid]] had a few KickTheDog moments in his past, his sheer [[PsychopathicManchild childlike dorkiness]] and deep seated complexes and neuroticisms tend to obscure that.
* Santa Claus and Mrs. Claus take on this role in ''Webcomic/SluggyFreelance''. They never do anything evil (well, except for accidentally destroying Tokyo that one time), they just happen to be engaged in a long running feud with the strip's resident NominalHero, Bun-Bun.
** Doctor Schlock, cornered by constant pursuit from Hereti Corp, eventually takes it over to protect his own life by becoming the BigBad.
** Sir John Jacobs, BigBad of "Oceans Unmoving", just wants to ensure a stable, living time bubble and society in Timeless Space. [[KillerRabbit Bun-bun]] by contrast is far more villainous in motives and methods.
* Professor Broadshoulders from ''ZebraGirl'' counts. He wants to banish Sandra to Hell simply because she's part demon, but he honestly believes she's a threat to the people around her. He spent his life fighting demons, Buffy style, to protect people.
* Shadow the Hedgehog from the British ''SonicTheComic'' continuity (not the games) is a clear example of this, being Sonic's EvilCounterpart. [[SonicTheComicOnline (This is in the unofficial online continuation of the original paper-and-ink comic book.)]] As such, Sonic is arrogant, boastful, and hot tempered, whereas Shadow is humble, polite, and focused, even managing to pull off a HeroicSacrifice against the heroes in his last scenes. Sonic has become a little less of an asshole lately, maybe realising that people are having trouble working out who's the good guy.
* Gen. William Howe in ''TheDreamer''. He really doesn't want to fight the Americans, but he has to follow orders.
* Redcloak, TheDragon and resident WellIntentionedExtremist from ''Webcomic/TheOrderOfTheStick''. Redcloak and his entire species (goblins) are the victims of JerkassGods who created them for the sole purpose of being XP Fodder, and declared that [[AlwaysChaoticEvil all goblins are evil]] so that the followers of those gods could then slaughter goblins guilt free. Redcloak himself is the survivor of a raid by KnightsTemplar paladins that slaughtered most of his family and community, and is intelligent, well meaning, has [[EvenEvilHasStandards kept his standards]], is repulsed by acts of {{Card Carrying Villain}}y, and, as the spiritual leader of all goblins, is trying to improve their lot in a world where, most of the time, they are attacked or killed on sight (by committing an act of BlackMail against the gods by threatening to unleash a world destroying, god killing EldritchAbomination, as you do). To some degree, Redcloak even seems to have WordOfGod on his side, as author Rich Burlew has stated "Some people choose evil, and some are driven to it by what life has forced them to endure. [[BigBad Xykon]] is not one of these. Redcloak, however, might be."
** Miko is an antivillain by WordOfGod - Rich Burlew actually used the word in a post on the Giant in the Playground forums: "In my mind, Miko is an antagonist, simply because she is an obstacle that the true protagonists of the story (the OOTS) must deal with/overcome. I think of her kind of as an 'anti-villain', a person in the villain's role who is not actually villainous." This sums up the trope quite nicely. In trope definitions, though, she's somewhere between this and HeroAntagonist. She genuinely believes she's doing the right thing (saving the world, protecting Azure City), and was stated to be a functioning paladin most of her life meaning she wasn't exactly jumping off the slippery slope before the end, but [[ArsonMurderAndJaywalking she frequently resorts to violence, is abrasive, and doesn't make funny one-liners while doing so like our heroes do]].
* Grace's brothers from ''Webcomic/ElGoonishShive'', [[spoiler: [[HeelFaceTurn at first]]]]. Abraham, as well.
* {{Webcomic/Snowflame}} seems to be going this way in the webcomic of the same name, although its too early to tell which Anti-Villain subtrope he will fall into. He seems to have some compassion for civilians and [[spoiler: tries to save Arkham Asylum after it is flooded with fear gas, even setting aside differences with Green Arrow to do so.]]
* King Radical of ''Webcomic/TheAdventuresOfDrMcNinja'', as seen [[http://drmcninja.com/archives/comic/20p75 here.]] For those who don't know, King Radical is the one in the red and yellow suit. Yeah. ''That'' is the BigBad.
* Adina from ''Webcomic/{{Zoophobia}}'' is often seen as a villain, but in truth, is actually intending to do what she believes is the right thing, which is essentially [[spoiler: killing all those who she deems as "evil" or "sinners" (which includes a [[AntiAntiChrist certain main character]]...)]]
** This basically leaves her along the lines of a WellIntentionedExtremist.
* Matthis Quigley from ''{{Unsounded}}''. He's a PunchClockVillain working for the Red Berry Boys who's OnlyInItForTheMoney. While his boss, Starfish, is a monster who's willing to cut out childrens' organs to transport some kind of illegal pymaric substance in their bodies, Quigley flat out refuses to work with the man [[WouldNotHurtAChild unless all of the children are freed once their job is done]]. He also has a MoralityPet in his eight-year-old, blind son, Matty, a tragic backstory where Aldish nationalists murdered his wife for treason, and a few PetTheDog moments, such as when he refuses to execute the captive Crescian peaceguard captain, [[HeroAntagonist Toma]], despite the captain's efforts to arrest them.
* Wizard from ''Webcomic/AccursedDragon''. He is made out to be a villain, but is {{Neutral Evil}} at worst.