A few characters experience this in A Triangle in the Stars, but the most prominent one is Bill Cipher. It's cemented by Chapter Thirty-Two, where he throws his plans to backstab Steven Universe away, having found he could no longer go through with them.
Other characters are Pyronica, Gabriel, and the Void. Keyhole, maybe, but he was less evil than a little misguided.
Through Gaia's machinations, Fortuna in Co-op Mode. As of the latest chapters, the same goes for Lisa.
Fortuna: "My name is Fortuna. There are 5,023 steps, or 2 years 2 months and 16 days left until the world is safe. On that last day, that last step, Cauldron will burn and, by my choice, I with it."
This is the very basis of Honor Trip, where Cell gets hit on the head, gains a sense of humanity, and turns good.
Zonoya herself in The Legend of Spyro: Zonoya's Revenge. It takes Malefor's demise and Cynder willingly allowing her to read her mind to see what Malefor really was to convince her to change. While Cynder is willing to forgive and try to help Zonoya change, Spyro still hasn't accepting the change. Spyro's actions may have be leading her to turn evil again when he attacks her son (due to him being Malefor's child), causing her to seek revenge for that. But in the end, she is stopped from going back across the line and ends up on fairly good terms with the heroes.
Miranda in the W.I.T.C.H. fanfic Kieva Lynn's Season Three, episodes five and six. While the cartoon didn't give her any backstory at all, this story fleshes her history out in a way that makes the experience that triggers it plausible.
In James Bond fan film Diamonds Cut, it's Lara Brooks. As an employee of traitorous MI-6 agent, she was originally going along with his plan, but eventually rescued Bond from allegedly certain death.
Frozen: A shtick of many Prince Hans redemption fanfics. It takes a great deal of Heel Realization for him to realize that Love Redeems and that there's more to life than just pursing thrones or power in general. As a kid, he was neglected all his life, causing him to develop a twisted mentality in that if you want to succeed in life, then you would have to lie and manipulate to get you they want. Concepts such as love, morality or compassion are seen as signs of weakness when you have a Social Darwinist mentality, where only the fittest survive.
Mega Man ZX Enforcers has so far had six of these: Atlas, Thetis, Aeolus, Siarnaq, Prometheus, and Pandora. The former four have theirs in circumstances that cause them conflict: Atlas breaks down crying when her childhood friend tells him to shoot her, but he comforts her and forgives her for her past (cementing a Relationship Upgrade in the process), Thetis finds out that the humans he thought were destroying the planet actually cared about it by undoing damage done by one of the Pseudoroids commanded by his "boss", Aeolus finds out that Model D completely duped him into helping it and sent its own soldiers after him, making him the one thing he hates (a fool), and Siarnaq aids Grey when he attacks Forrest and Shade (the same people who left Siarnaq for dead in the past) for using him, realizing that his stoicism was a mask for his fear. Prometheus and Pandora had theirs off-screen, choosing to aid the good guys (sort of; they've only helped them once so far) to avoid being recruited by Model D. Model O being used by Taylor might count too, since it's based on Omega, the Devil Reploid who was a major driver of the Elf Wars in the Zero series. And the HFT count is now up to seven, with it being revealed that Taylor himself was the one who created the Model S Biometals, but defected after being freed from Model D's influence and is now working on a secret weapon to destroy all the artificial Biometals he created.
The Monsters, Inc. fanfiction Angela's Pet Monster has Randall getting adopted by a human girl named Angela. He grows to like her, and eventually turns against Waternoose and becomes allied with Mike and Sulley.
He gets another one in the Simpsons crossover fic, due to Lisa's influence.
The Star Trek fic Safe and Sound has Khan, of all people, pull one when he realizes it would help his family and allow him to be with his new surrogate daughter, Lucille.
In Wanted, a Thor fanfic set during the second film, Loki doesn't fake his death and ends up helping Thor and the others defeat Malekith in London. He decides to stay on Earth with Thor after Darcy befriends him.
In the Naruto/TMNT crossover fic, Teenage Jinchuriki Shinobi, Kin shifts over to Konoha after realizing that Orochimaru would not be coming back for her, as she was simply a tool to him. Also, Karai originally planned an Enemy Mine instead, but follows the trope straight when the Shredder is defeated for good, knowing he'll never come back. Kabuto falls under a Heel–Face Brainwashing
Silver Spoon in A Hairier Problem: Rise of the Furball begins questioning if she should stay with Diamond Tiara and Fair Vista when the latter shows herself to them both for the first time. She comes to realize that it isn't worth it when Apple Bloom risks her secret and her life to save Spoon from a sudden flood in Ponyville, and she fully turns away from the pair once she realizes the full extent of their most recent plan to "expose" Apple Bloom when in reality Fair Vista wants to possess Apple Bloom and get revenge on Applejack and company for killing sable Loam.
A New Chance Series: Jessie, James, and Meowth leave Team Rocket after Ash rescues their Pokemon from Rico, and Brock lectures them about the nature of their jobs, their total failures, and tells them they are perfectly capable of being decent people, but are hopeless if they go back to stealing.
The Lion King Adventures: Recurring Series 4 villain The Interceptor has one of these gradually in Series 5. After fighting alongside the heroes first to defeat his former ally Shocker and then to save the world from Virusi and his master the Writer, he comes to bond with them, ultimately being considered a friend by Simba who lets him stay and live in the restored Pride Lands.
Young Justice: Darkness Falls features two. One was well built up, the other...not as much. But nonetheless, Big Barda and Supergirl both eventually come to see just how wrong they were in serving Darkseid, and join the heroes of earth in their war.
Super Sentai Vs Power Rangers The Liveblog: Tranza becomes rather nicer throughout the fanfic after watching Rika's descent into insanity and despair, eventually sympathizing with her. Near the end of the liveblog, he even tries to have Rika escape from Radiguet's wrath and call out his former ally over his plan.
In Pretty Cure Perfume Preppy, Lapinyuu is fired from Karlix for sporting Pretty Cure paraphernalia in Raflesina's presence and desires to join the Cures but is rejected, though by chance she winds up in her first acting job immediately afterward—as Third Ranger to Hearty Pure, Glowy Radiant.
In The Powerpuff Girls fanfiction Ladder, Princess Morbucks stops doing criminal acts and attempting to be a Powerpuff Girl after both Blossom and Buttercup die. Princess and Bubbles become each others Only Friend afterwards. Sadly, Bubbles later strangles Princess to death due to believing she was faking everything.
In Never Again, none other than Adolf Hitler himself gets this after a rebellion by the whole Nazi Party, led by his own second-in-command Heimlich Ritter, who was against his plans the whole time. Let this sink in. ADOLF. HITLER. GETS. A. HEEL. FACE. TURN.
In the Lilo & Stitch fanfic The Fire of Futures Past, Leroy escapes from prison and takes a very hard crash landing on Earth. He crashes the Pelekai 'ohana's family fun night, but he's too shook up from the crash landing to attack anyone. Lilo takes advantage of this and convinces him to tell a campfire story about Stitch (as the 'ohana have been doing throughout the night), and Leroy tells a love story about Stitch and Angel. From there, Leroy starts to care about the 'ohana, and they actually grow concerned for him as the United Galactic Federation comes to retrieve him. Thus, the main story shifts from the 'ohana just telling campfire stories about Stitch to also trying to prove to the Grand Councilwoman that Leroy has redeemed himself and should stay with them on Earth.
The sirens discover the ability to draw from Power of Love, a stronger source than the traditional Power Of Hate, tighten their family bonds; and are put on the path to this before the events of Rainbow Rocks even happen.
Destroyah at first didn't even understand what feelings like love, happiness, or friendship were until being forced to experience them in Equestria. After a long time, she decides she likes this sort of existence better than being a slaughtering living weapon.
Xenilla is eventually revealed to be Good All Along, his previous actions having been as a Well-Intentioned Extremist and acting as a smug villain to force his brother to grow strong. After a severe pride breaking spree, he finally decides to drop the act and atone.
Moonbeam Glimmer's Freudian Excuse put her on the path of a fear mongering antagonist to Godzilla Junior, convinced he would turn on Equestria and lead to catastrophe. After finding out they are Not So Different and Junior forgives her for her actions, she stops.
This Bites!: Given the Gray and Grey Morality of One Piece, this is a little shaky, but after witnessing the political pettiness of their superiors, Smoker, Tashigi and Hina outright tell Cross that they want to ally with him to bring down the World Government. As of chap. 42 Captain T-Bone, Vice-Admiral Jonathan and Vice-Admiral Tsuru join them in treason.
In Princess Trixie Sparkle, after spending the first half of the story steeling Twilight's identity and trying to manipulate things for her own personnel gain, Trixie eventually does this, after Astelle the true mare behind everything reveals herself and even becomes a new Element of Harmony!
In the One Piece/Steven Universe crossover A Gem in the Rough, Steven manages to convince Mr. 5, Miss Valentine, and Miss Goldenweek to abandon Baroque Works. This leads to them joining along with the Straw Hats for the remainder of the story.
In Pain of Parting Lucius Malfoy decides to join the light side after Snape's apparent death. The fact that eight nameless Death Eaters were killed directly by Voldemort before this is a consideration as well.
The Naruto fanfic Son Of The Sannin has this for Zabuza and Haku. The former appears as a mercenary during the Uchiha Insurrection, but instead of being killed is given jail time with chance for parole on the condition that the latter becomes a student in Konoha's ninja academy, culminating in him becoming Naruto and Hinata's teammate upon graduation.
Child of the Storm has a couple examples. Loki pulled one of these offscreen before the story started, thanks to his family. However, he's very much Reformed, but Not Tamed. In a more dynamic example, Maddie Pryor/Rachel Grey is introduced as a Living Weapon in Ghosts of the Past, the sequel, but The Power of Love (and a few of the Endless) help her to overcome her conditioning, culminating in being deemed worthy to lift Mjolnir!