Raimundo in Xiaolin Showdown, though that's after he did a Face-Heel Turn. He actually does suffer some consequences and trust issues afterwards because of it.
Subverted in Avatar: The Last Airbender : Prince Zuko is given tons of reasons to change sides in the second season finale, including the "encounter with the All-Loving Hero," Katara, after being put through hell all season:... and then doesn't. Wham!Remorse from that decision prompts him into a genuine Heel Face Turn half a season later in "Day of the Black Sun," and Zuko being Zuko, he takes the time for Calling the Old Man Out before he leaves. So a Double Subversion, all in all.
Mai and Ty Lee follow suit in "Boiling Rock". Mai's especially was epic, showing up like a Big Damn Hero and pulling off a Crowning Moment Of Awesome, while Ty Lee's just came straight from behind a tree (though disabling Azula is still awesome).
One of the earliest examples in the series is the forest spirit Hei Bai. He began rampaging through a village after his forest was destroyed, but Aang reassured him that it would grow back. After that, Hei Bai was a valuable ally to Aang.
The sequel series The Legend of Korra: Desna and Eska do this in the Book 2 finale "Light in the Dark", when they join forces with their cousin Korra and the crew in order to defeat their father Unalaq (who had merged with Vaatu) and the dark spirits at the Spirit World.
Transformers: Beast Wars has a number of examples. Dinobot and Silverbolt spent relatively little screen time as heels, but Dinobot was a pretty slagging well-done heel. More literal examples are: In the third season, Blackarachnia, and, near the end of the series finale, Dinobot's Transmetal 2 clone.
In Transformers Armada, Starscream (who seemed to be more based on Dinobot than the original Starscream) switched sides to the Autobots once Megatron got fed up with him being The Starscream. While Starscream originally only joined to stick it to Megatron, he hit it off with the kids and slowly became more accepted. Later, he would turn evil again and flop around to every "side" imaginable on the show. Eventually, he decided the threat of Unicron necessitated all of the Transformers uniting together and sacrificed himself to make Megatron realize that. He was recognized as a hero for his dying actions.
G1 has Jetfire/Skyfire (comics and cartoon, respectively).
In the cartoon, Skyfire (renamed due to the changes made to his animation model to distance the character from his toy's Macross roots) was a non-aligned Transformer from before the war, and old friend and colleague of Starscream's, who was lost when the two were deep space explorers visiting prehistoric Earth millions of years before the Ark crashed on it. When the Decepticons found him frozen in the Arctic, Starscream initially convinced him to join them, but the Autobots and their human allies convince him to turn against the Decepticons.
In the Marvel comics, Jetfire (using the toy's name but still having the animation model) was built on Earth by Shockwave, but Buster was able to gain control of him using the Creation Matrix and free Optimus Prime, who later used the Matrix to give Jetfire life as an Autobot.
The Transformers Prime Movie had two. The first one being Knock Out, in which it took some time for him to finally act like a true Autobot. The second one is Megatron of all decepticons. Having seen true oppression in the form of Unicron possessing his body, Megatron disbanded the Decepticons and left for parts unknown.
Tohru and Viper in Jackie Chan Adventures. Tohru's reason for changing sides is hilarious: Section 13 serves free donuts on Thursdays.
In ReBoot, Hack n Slash are a prominent example, joining the protagonists after Megabyte gets them destroyed and Phong rebuilds them, and them realizing that they missed having Bob around to stop them before they actually did anything really bad. Hexadecimal also undergoes profound change in the latter seasons.
Wouldn't you switch sides if your enemy put you back together after your boss sent you to the front lines to get destroyed by his sister simply to get rid of you?
In Liberty's Kids Sarah went from a fierce Loyalist to an American Patriot after seeing firsthand what the Americans went through in their fight for liberty.
In The Adventures of Super Mario Bros. 3, this happens to two one-shot characters. King Windbag went from a ruthless bully to a benevolent ruler and Crimewave Clyde renounced his criminal ways (though he graciously returned to prison, not wanting to spend another second with the Koopas).
A more recent Wrestling-themed episode played this trope closer to it's origins, as Grandpa's wrestling character, a notorious Heel called "Gorgeous Godfrey" turns into a Face "Honest Abe" right in the ring when he found out Bart was loving the Heel lifestyle a bit too much.
In one episode of Johnny Bravo, an evil doctor and his pet kitten steal Johnny's blanket and after hearing Johnny's speech on what the blanky meant to him, the kitten makes a Heel Face Turn and attacks the doctor.
Subverted with Sergeant Hatred from The Venture Bros.. He switched sides, going from an antagonist to a protagonist. However Venture Industries is just as immoral as the Guild, it's just the Guild admits and embraces this, whereas Dr. Venture doesn't even realize this. (Though at least he's trying to quit being a pedophile.)
Taken in a dark direction with Gary (formerly known as 21), he joins SPHINX and quits working for the Monarch. Yet The Monarch misses him so much, he's in denial about it and still thinks he's working for him. While Sgt. Hatred didn't trust him because he also thought he was still a henchman of the Monarch and the rest of SPHINX wasn't sure about him either at first. Gary, after realizing Good Feels Good, also went out of his way to catch a bad guy even though no one told him to, only to ruin Brock and Shore Leave's undercover mission. It's implied in-series this happened more than once by Hunter which causes Hunter to want him off the team. Sooner-or-later Gary accidentally hiring the old SPHINX back, making it so that they steal their mode of transportation and try their hand at evil once again and feels guilty about this. And Brock and Shore Leave end up feeling sorry for him because of it. In the end he decides to start henching for the monarch again.
Mildew Wolf was originally the scheming antagonist of the "It's The Wolf!" segments of Hanna-Barbera's "The Cattanooga Cats", and was constantly trying to trick the protagonist, Lambsy, into becoming his next meal. He was later recast, in the Hanna-Barbera ensemble showLaff-A-Lympics, as a friendly (albeit cynical) sports commentator, with a strong dislike for the Really Rottens' underhanded shenanigans.
Xanatos is debatable. He was at worst Lawful Evil and at best a morally ambiguous Enemy Mine who would team up with the Gargoyles in cases of Evil Versus Oblivion. Xanatos is opportunistic above all else, and it could be argued that he sees the Gargoyles as valuable allies.
The Bee Keeper from Johnny Test pulls a rather reasonable one after Johnny, Susan and Mary find a way to get children to appreciate his natural honey candies by having him distribute them free once a year on a new holiday — they had been spending the entire episode trying to establish a new "Free Candy" holiday and continually failing due to various obstacles; ones the Bee Keeper pointed out wouldn't apply to him and his candies once he discovered their plans. Since he gets what he wanted from the beginning and the protagonists helped him do it, he's content to give up villainy.
The Brain Freezer pulls a reasonable one as well after Johnny, Dukey, Susan, and Mary help him with his looks (and other issues) long enough for him to make the ice coffee cafe he's always wanted. He doesn't exactly become a good guy, but instead a Chaotic Neutral that competes with Johnny rather than be a direct antagonist in later episodes.
Mr. Trudge in the 1980's Jonny Quest episode "Creeping Unknown" after the Quests discover the plant monster's weakness (it's sunlight, for some reason). He was only being forced to help the monster, anyway. Or so he claimed.
Early in Ninjago, Lloyd Garmadon, the son of malicious Lord Garmadon, tries his best to be a villain, but in hindsight, he's just a mischief-making little kid. After many mishaps and his worst mistake of all, releasing Pythor, Sensei Wu decides to put Lloyd back on track by treating him as if he were his own son. Lloyd drops the "bad guy" routine in a heartbeat, but still remains a troublesome prankster.
Arthur Binky Barnes started off as a bully, but later became a friend. To a lesser extent, Prunella also fits.
Molly and Rattles fit very well too. Originally they were even worse than Binky, but later on they became nicer.
Riven in Winx Club decided to side with the Trix after one too many arguments with the Winx and his fellow Specialists. He joins the heroes when the Trix reveal they were just using him.
The Earth fairies stop trying to destroy humanity when the Winx show them that not all humans are bad and convince their queen Morgana to drop their crusade.
Star Wars: The Clone Wars: Nossor Ri and the entire Quarren army at the end of the Mon Calamari Arc in Season 4, General Tandin and several of his soldiers in the Onderron Arc in Season 5.
About half of the villains in the old My Little Pony And Friends series from the 1980's would at some point become good, including Katrina, Sting, King Charlatan, Porcina, Crunch The Rockdog, or the gnome from "The Magic Coins".
As for the current series, Princess Luna became good again after being purified by The Elements Of Harmony. And after two years, Trixie returned to take revenge on Twilight Sparkle, but at the end she finally learned her lesson and left Twilight on good terms... sort of. She's far from reformed and even her apology makes it somewhat clear she may not be a complete face yet.
Later, Princess Celestia assigns the Mane Six to put Discord through one of these if possible. To the surprise of everyone, including Discord himself, they succeed, to an extent- it's made abundantly clear by both dialogue and Word of God that this is less of a reform and more of an uneasy truce. Discord is the embodiment of Chaos after all.
Super Friends. This happened at the end of almost all of the 1973/74 episodes after the Super Friends explained to the villain(s) the errors of their ways. It usually involved the villain sincerely apologizing and promising to change their behavior. Examples: Doctor Rebos in "The Androids", Professor Baffles in "The Baffles Puzzle", Minimus Mole in "The Mysterious Moles", Anthro the alien in "The Power Pirate" and Dr. Shamon in "The Shamon U".
In NFL Rush Zone Guardians Of The Core, both guardians Ash and Ricky started off as agents for the current Big Bad, only later joining the heroes when it they finally realize their mistakes and try to make up for them.
Teenage Mutant Ninja Turtles (2012)'s incarnation of Slash is depicted as a Well-Intentioned Extremist, who wants what he thought was best for Raphael by killing his brothers. After being defeated, he fled and joined forces with the even more psychotic Newtrailzer in fighting the Kraang. However once Newtralizer's plan of Kraang-eradication involving killing several innocent humans, Slash became disgusted and ultimately re-joined Raph in taking him down. Mild example, but very apparent by his more heartfelt parting with the turtles.