In The Gamer's Alliance, Abel makes this very clear by adapting the name Cain once he's turned to the dark side. The heroes are oblivious to his new, treacherous nature and think he's only acting emo because of his embarrassing encounter with a lustful mage earlier in the story. Refan and Ronove also make a FaceHeel Turn later on when they side with demons.
Corey from Three In The Afternoon does this not once, but twice, taking full advantage of his more idealistic friends the second time around.
Julia van Helden does this in KateModern in response all the traumatic experiences she suffers while helping the K-Team, and out of misplaced love for a villain.
In Associated Space, Nazar actually defeats Fatebane, captures him, and brings him to the villain. However, when he doesn't get paid, he decides to break the hero out, inadvertently joining Fatebane's side.
Reynold, of Homestar Runner's Show Within a ShowThe Cheat Commandos, recently went over to work for the evil forces of Blue Laser. All things considered, it was surprisingly plausible.
Any time a previous non-player starts to actively participate in the 'game' in Survival of the Fittest. As you might imagine, this tends to happen a lot.
Agent Washington of Red vs. Blue. Thankfully, it's temporary.
Ephram from Dead Ends does this when most of his family is killed by zombies and Eddie's stray gunshot.
Alex of Marble Hornets does this somewhere between seasons 1 and 2 by appearing to work/cooperate with the Operator, though it's made explicitly clear in season 2's finale that he's no longer any friend to Jay and Jessica. Of course, certain circumstances may have led him to that end.
MSF High: The biggest example would be Gestell, due to his split personality issues, being revealed as the villain of one arc. It's not The Mole, as he had shifted away from hanging out with the players, and did not sabatoge their efforts using this.
Ma-Ti and the Cinema Snob in To Boldly Flee. Temporarily Nostalgia Chick and Todd when they're assimilated by Mecha-kara.
In Worm, there are a few cases of heroes opting to become villains (Accord and Flechette being the obvious ones), but the most interesting case comes when Scion switches from fighting for humanity to destroying it.
In The Sonic Amigos episode Detective Knuckles: Cheez it Dilemma (part 1) Sonic turns evil because he felt like it. At the end of part 2, Sally scolds Sonic so badly he becomes good again.
In Pokémon Rusty, Rusty is roped into joining Team Rocket, but backs out pretty quickly. Beedrill becomes the new boss of Team Rocket.
C0DA, written by former The Elder Scrolls series writer/designer Michael Kirkbride, takes place in the far distant future of TES universe. It includes several characters who have appeared in the series previously. In particular, Yagrum Bagarn, the last living Dwemer who greatly assists the Player Character in Morrowind, is now the Arc Villain "The Intellective". He is trying to invade the reality of the work by spreading his "Videoverse" into it. The introduction of the "Pseudo-6th-House" (essentially a super team of Physical Gods) has them working to stop him.
My Dad's Tapes: Melissa, after giving Chris important information about his father and acting as a friend, willingly joins up with donotcontinue thanks to an interest in his work.
After Tissue's elimination in Object Overload, we can see him reading a photo album called "Memories, looking at how Lighter betrayed him, as well as burning a hole through him and wadding him up, causing his current appearance. Lighter continues to bully Tissue after the incident.