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.
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.
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