Baron Klaus Wulfenbach from Girl Genius. 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 mad science-induced anarchy. If not for his employees and his willingness to experiment on Othar Tryggvassen (Gentleman Adventurer!)'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 here.
The protagonists of Narbonic are prone to attempted (and sometimes succeed) murder on each other at a moment's notice.
The cast of The Last Days of Foxhound, excepting Ocelot and 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 Punch Clock Villain 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 Liquid had a few Kick the Dog moments in his past, his sheer childlike dorkiness and deep seated complexes and neuroticisms tend to obscure that.
Santa Claus and Mrs. Claus take on this role in Sluggy Freelance. 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 Nominal Hero, Bun-Bun.
Doctor Schlock, cornered by constant pursuit from Hereti Corp, eventually takes it over to protect his own life by becoming the Big Bad.
Sir John Jacobs, Big Bad of "Oceans Unmoving", just wants to ensure a stable, living time bubble and society in Timeless Space. Bun-bun by contrast is far more villainous in motives and methods.
Professor Broadshoulders from Zebra Girl 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.
Gen. William Howe in The Dreamer. He really doesn't want to fight the Americans, but he has to follow orders.
Redcloak, The Dragon and resident Well-Intentioned Extremist from The Order of the Stick. Redcloak and his entire species (goblins) are the victims of Jerkass Gods who created them for the sole purpose of being XP Fodder, and declared that 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 Knights Templar paladins that slaughtered most of his family and community, and is intelligent, well meaning, has kept his standards, is repulsed by acts of Card Carrying Villainy, 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 Black Mail against the gods by threatening to unleash a world destroying, god killing Eldritch Abomination, as you do). To some degree, Redcloak even seems to have Word of God 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. Xykon is not one of these. Redcloak, however, might be."
Miko is an antivillain by Word of God - 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 Hero Antagonist. 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 she frequently resorts to violence, is abrasive, and doesn't make funny one-liners while doing so like our heroes do.
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 tries to save Arkham Asylum after it is flooded with fear gas, even setting aside differences with Green Arrow to do so.
Adina from 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 killing all those who she deems as "evil" or "sinners" (which includes a certain main character...)