In Worm the main characters are a group of supervillain called the Undersides, but they have good intentions (except for Regent). Skitter is a supervillain because she couldn't betray her friends and because of Jerkass superheroes, and constantly tries to protect people, Tattletale is also one for protecting people, Grue got the job so that he could look after his little sister Imp and Bitch can't empathise with humans but genuinely loves dogs and supervillainy funds her shelter. They also serve as A Lighter Shade of Blackagainst the truely evil, and stop about as many villains as the heroes. But it's part of a plan to take over the city!
Fury Of Solace, originally created for the ELE application contest note he didn't make it onto the DVD despite a fantastic song, probably because he really isn't evil. His Villain Songnote linked above 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.
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 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.
Red vs Blue has Agent Washington who is only after the Blood Gulch crew to take Epsilon back to the Chairman so he doesn't have to go to prison. Adding to this, the only reason he has to get Epsilon in the first place is because Caboose didn't turn Epsilon in like Wash told him to.
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.
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 Gamers 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.