In Kill la Kill, Ryuko is brainwashed by the Life Fibers into thinking that Ragyo was a loving parent, puts on Junketsu (then has it sewn onto her body so she can't take it off), and starts going after Satsuki. Luckily, the combined efforts of all the remaining good guys help her snap out of it.
Shu in Guilty Crown has one of these after Hare is killed, abandoning his faith in being a kind leader and becoming harsh and brutal to never let such a tragedy happen again. Itīs later revealed to be a mask he puts on to help the efficiency of the trapped school, and he abandons it after most of the selfish students gets murdered by Gai.
Kaiser Ryo following a textbook Freak Out in Yu-Gi-Oh! GX. The dub even has Judai/Jaden compare this to, "when a pro-wrestler suddenly starts dressing in black and throwing chairs in the ring." Judai, like his predecessor in Yu-Gi-Oh!, also temporarily turns to The Dark Side (hey, Superpowered Evil Sides take some getting used to).
In 5D's we have the Dark Signers, although whether Rudger - their leader - was ever on the side of good to begin with is questionable.
Vegeta from Dragon Ball Z, who was admittedly already a Heel-Face Turn and technically just returning to his original alignment, went through yet another Heel-Face Turn after the showdown of rivals. The whole arc also has the bonus of being a mid-life crisis as well as being a Not Brainwashed moment. Come to think of it, he is probably the one character in the entire series to do as many alignment changes as a pro wrestler.
It could be argued that he never switched sides at all, as he's always been on the same side: his own. Trusting him is the fault of the heroes.
Heppokomaru/Gasser in the manga sequel of Bobobo Bo Bobobo. He comes around eventually, though. This fact is made more infuriating when everyone discovers that the reason he betrayed Bo-bobo and his group was in order to save his sister, who joined the empire of the Big Bad on her own, and is rather unpleasant in the personality department.
Happens very briefly in the manga adaptation of Slayers: Evolution-R with Zelgadis.
We know that Griffith from Berserk is a bad guy at the start of the anime, but most of us wouldn't know this from the idealistic mercenary leader that we meet in flashback during the second episode, who is about as close to a Messianic Archetype as one can get in a series like Berserk. The anime, which follows the Golden Age manga arc of the series, is about Guts's time with Griffith's Band of the Hawks, and the events that lead up to Griffith's betrayal, his ascension as the fifth member of the Godhand, and Guts's circumstances in the very first episode. And when Griffith finally does go bad in the final episodes, hegoesvery, verybad.
Code Geass has enough Face-Heel Turn and Heel-Face Turn to drive one mad. By the end of the series everyone has switched to someplace at least once and some have done it two or three times do really screw your list over. Practically the only character never to change sides is C.C., who was on her own side from Day 1 and just followed Lelouch out of obligation.
What's really infuriating is that you can't even tell which side is good and which is bad. They're both morally ambiguous chessmasters with roughly the same plan for world peace.
Walter C. Dornez, loyal aide to Integra Hellsing in Hellsing, first seems to do a Face-Heel Turn against his will after been brainwashed by the villains, but is later revealed to have been a willing traitor since WWII. However, he later did a Heel-Face Turn by killing Doc, complete with Redemption Equals Death.
The Uchiha Bros. (tm) from Naruto might be taken into account, though their Heel turns were not really an alignment change. Maybe except for Sasuke's latest.
Obito Uchiha, who was basically the Uchiha version of Naruto, have the philosophy of protecting one's comrade, have the dream of being a Hokage, and died to ensure his friends survive... is the Big Bad Tobi.
Julia and Collins from Blood+, though the former does return to the side of good after a while. The other gets a bullet to the brain.
Post-Time Skip Rossiu, previously a good guy, sets up Simon as a scapegoat for the problems caused by the Anti-Spirals and takes over the government - and his plan to survive the Anti-Spiral attacks involves leaving a large portion of the world's population to die.
The real Face-Heel Turn award doesn't go to Lord Genome, but to his daughter Nia, who was the unwilling messenger of the Anti-Spirals. The worst part? She had just gotten engaged to Simon.
Sasame in Prétear later joins the Big Bad to become her servant because he was in love with her and couldn't bear to fight her. The Big Bad herself also face heel turned due to love. Later they both undo this with a Heel-Face Turn to once again join the heroes.
In Soul Eater, Kim and Jackie do an unwilling Face Heel Turn under the influence of Arachnaphobia's insanity manipulation machine. The actions of Justin Law, however, appear for the time being to be genuine: killing BJ and framing Stein for the murder (though Medusa almost certainly had a hand in it), trying to kill Maka Albarn as her soul perception might uncover Asura for Shinigami. He also seems to enjoy taunting the imprisoned Death the Kid, and listens in when Gopher is beating the boy up.
Death the Kid apparently cracked under all of the pressure and torture and pulled a Face-Heel Turn of his own. Thankfully it was a very brief one; he got better thanks to Black Star snapping him out of it.
Wonrei joins the Faudo revival cult in Konjiki no Gash Bell!! when his bookkeeper is placed under a curse that will kill her if Faudo is not revived. However, this Face Heel Turn is fairly temporary, as expected given the nature of the series.
Megumi in Gate Keepers, after her envy towards Ruriko reaches its peak.
Panty & Stocking with Garterbelt: In classic Gainax fashion, Stocking slices Panty up into 666 pieces and reveals that she is a demon about a minute before the end of the last episode (whether of the whole series or just the first season is yet to be known).
Mikael from Tenshi Ni Narumon does a Face Heel Turn in the last episodes of the series which ends in an epic breakdown. He gets better.
In Puella Magi Madoka Magica, every witch apart from ex-familiars counts as this due to how magic works in the general universe, the most prominent in-series example being Sayaka becoming Oktavia Von Seckendorff after her Soul Gem darkened completely and turned into a Grief Seed.
While Witches can be given a pass in that they really have no say in whether they become evil or not, we get a straighter example in Rebellion, in which Homura friggin' Akemi pulls one, hijacking Madoka's powers to give her a normal life. While whether Madoka WANTS a normal life or not is debatable, what with her her losing her memories of the nightmare she had endured during the series and saying she DOES, the fact remains that Homura is now a self-proclaimed 'demon'.
Debatably happens in Gunsmith Cats when Misty Brown chooses to give up on Rally and instead go and live happily ever after with Psycho Lesbian Goldie, aka the woman who earlier brainwashed and implicitly raped her. Debatably because we don't know if she is doing so voluntarily or due to still being brainwashed.