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.
Lightning and Thunder both lampshaded and mocked the trope during the Harry/Quirrell first year confrontation, stating that "this wasn't some TV show where he could turn the bad guy good with an excellent well placed speech."
In James Bond fan film Diamonds Cut, it's Lara Brooks. As an employee of traitorous MI6 agent, she was originally going along with his plan, but eventually rescued Bond from allegedly certain death.
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 Angelas 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.