Batman villainess Catwoman has since reformed and become more of a hero than a villain, often teaming up with Batman on his missions.
The Catwoman of Earth-Two, an alternate universe in The DCU, also turned over a new leaf when she recovered from amnesia. Horrified, she was willing to go to jail for the crimes she had committed. When Batman sprung her from jail to help him, she revealed that she had lied; she had actually chosen to be a villain and then chosen to reform because she realized that it was her only chance for a normal life (whereupon they fell in love, got married, and had a daughter, Huntress).
The Riddler also performed a Heel Face Turn, but this too was prompted by amnesia (in Riddler's case, induced by a blow to the head). Additional trauma (from a bomb blast) later returns Riddler to the rogues' gallery.
The Joker of all people tried going straight in the Silver Age story Joker's Millions, not out of a desire to do good but simply because he'd been led to believe he'd inherited enough money to never need to commit crime again. This made more sense for the character back then when he was a villain with a gimmick rather than the elemental force of chaos he has become.
Two-Face in multiple incarnations has reformed and returned to his legitimate life as Harvey Dent (usually temporarily) following psychotherapy and reconstructive surgery. As Two-Face, he's almost by his nature a walking Heel–Face Revolving Door.
Flash villains the Pied Piper and the Trickster both reformed. The Pied Piper had always been the sort of villain who had stolen money for orphanages. The Trickster had pulled off a Deal with the Devil and escaped, and reformed because he couldn't do anything to top that, and didn't want to go to Hell when he died, after his trick. A recent apparent Face–Heel Turn was actually an attempt to pull off a Fake Defector trick — which turned tragic when they appeared to be in on the death of Bart Allen, the Flash. The Trickster is now dead, but the Pied Piper is facing Reformed, but Rejected.
The pre-Flashpoint Emil Hamilton was last seen under arrest for his actions as Mad Scientist Ruin. Here, he is working on S.T.A.R. Labs project to help pierce the dome surrounding Gotham City. Keep in mind Hamilton has gone through the Heel–Face Revolving Door quite a few times.
Also, there is Telos, who after learning of his true past of being an actual person rather than a living planet who was enslaved by Brainiac, decided to help the heroes against Deimos and declaring that all the captive cities should not die.
Superwoman in Convergence: Crime Syndicate, after reflecting on much of her life while on death row. And later during her fight with Wonder Woman from DC One Million, where she specifically wishes to save her city as a means of atonement for her criminal deeds and the accidental death of philanthropist Bruno Manneheim.
Around the time of Siege, Hank Pym tried to recruit Loki by citing the large number of former villains who ended up as members of the Avengers. This prompted in a What the Hell, Hero? from the rest of the team, since Loki is the fricking Norse god of evil.
Except he isn't, really. In Norse mythology, he's more of a mischievous trickster figure, and was even a close friend of both Odin and Thor, playing off as more of a guile hero than anything. He went through a Face Heel Turn after going through a vicious punishment for triggering Ragnarok in mythology, though. That said, the comic version is... less ambiguous.
Overdrive from Superior Foes of Spider-Man is smart enough that this trope is his entire reason for being a costumed villain. He grew up as a young boy who idolized superheroes, and reasoned that the quickest way to become an Avenger would be to start off as a villain and then eventually reform and fight alongside his childhood heroes.
Venom is a classic case of a Heel Face Turn to create an "edgier" hero. Also because Venom — created and illustrated by Todd McFarlane — was, for a time, considerably more popular than Spider-Man himself, being a giant, hulking, over-designed monster with zero qualms about killing. Quintessential '90s anti-hero, essentially.
The Rhino eventually went legit, turning himself in, serving his time, and getting released on good behavior before settling down with a doting Russian woman. It lasted all of one more appearance. The new evil Rhino killed his wife, sending him on a Roaring Rampage of Revenge. He put the costume back on, killed the new Rhino, and is back as a villain.
Back in the 80's, the Sandman got sick of crime and went straight. He actually joined the Avengers for a while. That lasted a good twenty years, real world time. Then his old teammate the Wizard stuck him in a machine and brainwashed him to be evil again. Sigh.
In the first ever Superman/Spider-Man crossover, Doctor Octopus does one of these when it's pointed out to him that Lex Luthor's planned actions will destroy the world: "Where are you going to spend your billions?"
Emma Frost's Heel Face Turn is proving permanent. However just like Jean, Emma suffers from the Never Live It Down trope. The story that cemented her position as a central X-Man was also the story in which the readership was first led to believe she betrayed the X-Men, just to discover later that she was being psychically manipulated by Cassandra Nova. Before having her own mind trapped inside an indestructible box, Nova had left a psychic impression of herself in Emma's mind, which was subtly manipulating her. That impression slowly twisted Emma's perception of herself, exploiting her survivor's guilt and making her believe she could never redeem herself. In the end, it was shown that Emma was willing to sacrifice herself so that Nova's plan wouldn't succeed. Besides that story, the only other time Frost fitted this role was during Dark Reign, when she joined Norman Osborn's Cabal, as part of her and Cyclops' plan to later make a fool of Osborn and guarantee the safety of mutantkind. Also, while part of the fanbase and some writers believe Emma is still not trusted by her teammates, there are many evidences pointing the opposite. For one, she's been banking the X-Men for quite some time now, and they're not uncomfortable with that. More importantly, she's been the main Cerebro user ever since Professor Xavier left, and the X-Men are ok with that (Cerebro is a machine able to boost one's telepathic power to impressive levels. By letting Emma use it, the X-Men are leaving their minds - and those of thousands of innocents - completely vulnerable to her powers, which says a lot).
For everyone but the three people who might remember that issue of ROM, it was the fact that her powers were driving her slowly insane and she was realizing that Mystique was both unable and unwilling to help, with a little nudge from Mastermind (who wanted to put the screws into Mystique by inducing her beloved foster daughter to run away) that did the trick.
There's also Sunfire, Banshee, Magneto himself, Marrow...
Magneto is the founder and leader of this continuity's version of the X-Men.
Sabretooth goes from a villain with standards to a genuine believer in Magneto's creed, a would-be atoner, and a surrogate father figure to Blink and Wildchild.
Sauron and Toad, both minor villains, are on the heroic side and loose allies of the X-men here.
Mystique ferrets out information for Magneto and runs a secret escape line for smuggling humans out of Apocalypse's genocide-zones... although she also remorselessly skims wealth from her "customers" as well.
Garganta from Femforce debuted as a villain. Popular with readers, she was brought back as a recurring character, with her original rampage being revealed as a side-effect of the experiment that gave her her powers. She eventually became an auxiliary member of Femforce.
The "Chinese Gods", or what remained of them, in The Great Ten. After Celestial Archer introduced them to his patron goddess, who told them that they were simply altered humans, Gong Gong, Lei Zi, Kuan Ti, Lei Kung, and Chu Jung decided that they would fight alongside the Great Ten.
Hellboy is one of the most glaring examples. From birth, he was destined to usher in the apocalypse under the name Anung Un Rama as The Antichrist. Instead, he wants nothing to do with it and becomes an Anti Anti Christ, going as far as to keep his demon horns filed down.
Powerplex in Invincible always considered himself a hero in his single-minded obsession with killing Invincible — but after Invincible left the planet for an extended period, he received counseling and a second chance as a member of the superhero team the Actioneers. However, when Invincible returned, he couldn't control himself and attacked him again. After finally accepting the fact that Invincible wasn't at fault for his sister's death and that the death of his wife and son were on his shoulders and his alone, Powerplex surrendered. In a later conversation with Cecil, Invincible learns that Powerplex was a real hero while he was away, and will be again after more counseling.
In the Irredeemable spinoff Incorruptible, former supervillain Max Damage realizes that The Plutonian'sFace–Heel Turn will now leave the general public without a true Big Good to defend them. In response, he decides that he needs to step up for the people and becomes Max Daring.
King Sombra does so the end of "The Siege of the Crystal Empire" arc in the My Little Pony: Friendship Is Magic (IDW) comics, after realizing he's become the monster he saw in the Crystal Heart from a thousand years prior.
The Transformers has a number of Decepticons leave the cause, in part due to the Adaptational Heroism the faction has had, and also due to the truly wretched participants in the group.
Thundercracker leaves the Decepticons in The Transformers: All Hail Megatron, after the slaughter of thousands of humans as well as the conversion of almost three thousand of their own men into monsters due to the Decepticon experiments.
After the events of AHM, Dirge leaves the Decepticons after they abandon him, and he and Swindle aid the neutrals and Autobots during the post-war upraising in The Transformers: Robots in Disguise. Similarly, Tankor and Squawkbox depart from the Cons as well as they felt the peace achieved with Megatron's defeat was more preferable to the fighting (Tankor himself went on to be a supporting cast member in the The Transformers: Windblade series).
The Transformers: Dark Cybertron ends with Megatron leaving the Decepticons, disillusioned with how far he'd fallen from his original goal of fighting for equality.
Ambulon became an Autobot after the Decepticons forcibly entered him into their (failed) combiner program, leaving him with the useless alt-mode of a leg in The Transformers: More Than Meets the Eye. In season 2 Ravage joins the Lost Light crew to stay by Megatron's side both out of loyalty and seeing the massacre inflicted by the more zealous members of their side.
In Violine, the doctor after being declared the world champion of the Pygmies. Van Beursen, Muller and Marushka later have amnesia-induced ones.