At least one major villain or rival (but usually more) per season in Yu-Gi-Oh! and Yu-Gi-Oh! GX; balanced by the fact that the opposite is none too rare, either. This is often combined with Defeat Means Friendship, but not always. (In fact, villains who are truly incapable of redemption are kind of rare in this series.)
Aside from Kaiba, who never became much more than a Jerk with a Heart of Gold to anyone aside from his brother, the earliest was when Pegasus from the original series allied with the protagonists following his defeat at the hands of Yugi, and the theft of his Millennium Eye by the evil spirit of the Millennium Ring, a.k.a. Yami Bakura. But that Heel Face Turn only happens in the anime; in the manga, Yami Bakura kills Pegasus when he takes his eye.
Ryuji Otogi/Duke Devlin was an odd example, because to many fans, his Heel-Face Turn made very little sense; one minute he was acting like the typical heartless villain, the next minute, he was apologizing for everything. Truth be told, the manga version of the story - where Otogi was used as an Unwitting Pawn by his Axe Crazy father, who was the true villain - made much more sense, but was far darker than the anime version and the adaptation was probably at a loss to explain the transition because it had to leave him out.
Another example is Tetsu Ushio from Yu-Gi-Oh! 5Ds. He started out as a Dirty Cop and a pawn of Rex Godwin, who, like most citizens of Neo Domino, had nothing but contempt for the residents of Satellite. It was never a case of Defeat Means Friendship (two defeats at Yusei's hands only made their feud worse) but he started mellowing around the Fortune Cup (realizing that Godwin was treating him like garbage played a big part) and he was officially Yusei's ally at the end of the first season, mostly after starting to sympathize with the Satellite residents.
In the Sailor Moon anime, the Ayakashi Sisters, Amazoness Quartet, and Professor Tomoe have Heel Face Turns and survive. Nephrite, Saphir, and Prince Demand have them and do not. The Amazon Trio have an odd in-between case, "dying" on Earth but getting to go live in Elysion (the world of dreams) rather than the afterlife.
There are several Heel and Face turns in Gundam SEED. Loyalties and what one fights for are driving themes for the entire series, in fact.
Loads of villains in Fairy Tail go through this. You can count on at least one Heel Face Turn per every major arc, and sometimes it happens to most of the current enemy team. Sometimes this is due to The Power of Friendship. Sometimes due to the villains being not that villainous to begin with, simply misguided or deceived.
And then there was the Fake Defector. We were all pulling for him, too!
Digimon has one every year, often used to switch plot arcs partway: Season 1 has Gatomon (Tailmon), Season 2 has Ken, Season 3 has Beelzemon (Beelzebumon), Season 4 has Koichi, and Season 5 has Keenan (Ikuto).
Season 3 also has Yamaki (the Hypnos guy), who functions as the initial main villain of the series, goes from being defined by his hatred of the "Wild Ones" to a staunch ally and sympathetic behind-the-action helper. There is also Antylamon, one of the Devas working for Zhuqiaomon, and Zhuqiaomon himself (the second main antagonist of the series).
There's also the manga: For instance, V-Tamer has Alias 3 and Neo Saiba, all four, do Heel Face Turns.
Season 5 also has Nanami and Ivan at the end, as well as the Royal Knights, Gotsumon, and Merukimon
Nene, Kiriha, and Yuu from Season 6. The rival hunters from its sequel also eventually pull one off.
Used twice in Naruto's "Land of Waves" arc. Traitorous ninja Zabuza and his androgynous young henchman Haku, whom he habitually mistreats, have been hired by gangster Gato to stop the Land of Waves villagers from building a bridge that will be economically vital to their island. Naruto and his friends are sent to make sure the bridge gets built. When Haku seems to kill Sasuke, Naruto swears revenge until he learns of Haku's tragic past, which calms him down (besides, Haku made sure that Sasuke is Not Quite Dead). Then, Haku does a Heroic Sacrifice to save Zabuza, and the rogue ninja's guilt over his abuse of his dead partner causes him to Freak Out; Zabuza switches sides, killing Gato before getting killed himself.
It's better than that! Haku dies nobly and Zabuza is unfeeling about it, and Naruto in the middle of a freaking ninja battle, freaks out at him about how much Haku cared and how wrong this is, until the Demon of the Mist turns around slowly...and there are tears running down his cheeks.
Zabuza: You talk too much...
Twice in the "Land of Waves" arc, but far more frequently later. Hyuuga Neji, who is half-inspired by Naruto's (an obvious All-Loving Hero) victory into rethinking his fatalistic Jerk Ass-itude and goes on to claim that Naruto saved him. Or Gaara, who is so stunned by Naruto's empathy and suckerpunch, that he stops living to kill people and begins living to help people, enough to become the Kazekage!
The sword didn't really go from bad to good, it was just helping the good guy for its own benefit. Plus, it seems to be with the bad guy again anyway. But now that its original owner has been Killed Off for Real...
570 has the Kyuubi/Kurama, who was thought of to be the very embodiment of hatred, finally give in to Naruto's kindness. The next chapter showstheresults.
In Chapter 627, The Greatest example of this trope in Naruto has occurred. That's right people, Uchiha Sasuke has decided to ally with the good guys..
Not only that but OROCHIMARU, the big bad of a huge number of early plot arcs has decided to join the fray as a good guy. Though his motives are ambiguous enough that it could just be an Enemy Mine.
Obito appears to be invoking this trope in the new 665 chapter. Though he was originally good to begin with.
And in chapter 667, Kabuto has joined the fray, helping to revive Sasuke. The reason? His time in Itachi's Izanami spell helped Kabuto realize his true nature, that he's really a good person deep down, and that he has a home to return to.
At this point, Madara is the only major villain that hasn't seen the light. It remains to be seen whether that will last...
Dragon Ball and Dragon Ball Z practically built its cast this way. By the end of the series, most of the heroes are former villains; it's easier to list the characters who didn't try to kill or at least beat Goku up when they met him than otherwise. For that matter, Goku himself had a backstory heel-face turn, when his inherent Saiyan nature was subverted by a blow to the head. It took Vegeta the longest to fully turn, and he actually turned all the way back to heel right before it happened.
To highlight it better, of the core cast of Z fighters from throughout DBZ, Goku himself had been sent to Earth initially to depopulate it as a mindless ape, Yamcha was a bandit who tried to rob Goku when they met, Krillin was The Rival for Master Roshi's attention, Tien and Chaozu were students of the Crane Hermit, a wicked rival to Master Roshi, Piccolo was the son/reincarnation of Evil Overlord King Piccolo out to avenge his father/former self's defeat by Goku, Vegeta came to Earth solely to steal the Dragon Balls and kill anyone who got in his way, Androids 17 and 18 were rebellious punks who caused a Bad Future in Future Trunks' timeline, and Majin Buu was a childlike pink blob monster who didn't even realize that causing death and destruction was bad until Mr. Satan set him straight.
In Saint Seiya, both Saga and Kanon have a Heel-Face turn. Saga, right before he kills himself, and Kanon after realizing that even after all he had done, (corrupted his brother and made him try to kill Athena, besides trying to flood the world by tricking Poseidon), Athena still saved him multiple times and cared about him. That made him turn into a Face and fight for Athena; Milo at first doesn't trust him, but after he attacks Kanon and the latter doesn't retaliate even once, Milo realizes Kanon has truly become good.
Ayaka Steiger in Kurau Phantom Memory turns from the main bad chasing the protagonists to their biggest ally after discovering that her boss ordered the murder of her father.
Nearly every villain in Kero Kero Chime. In fact, in a bizarre and random musical sequence in the last episode, Demon King Bao, the Sealed Evil in a Can who turns out to be the true reason most of the Hebizoku and Kaeruzoku disappeared 10 years ago, as he took them with him upon being banished, reveals that he's completely reformed, and he and his former enemies like being Trapped In Another World, as it's allowed them to become such great friends.
In StrikerS, seven of the twelve Numbers and Agito.
Princess Tutu has several characters who follow this trope. In the first season, it's Fakir (sort of) and Edel. And towards the end of the series Rue discovers that the Raven is not her true father, and risks her life to save Mytho.
Skyers 5 used this trope to good effect.
Rokudo Mukuro in Katekyo Hitman Reborn!, but it only half counts because his Heel Face Turn coincides with his possession of Chrome Dokuro's body
In D.Gray-Man, General Cross can turn Akuma good. This isn't perfect; they have trouble rejecting explicit orders from the Millennium Earl. To compensate, Cross has these Akuma rigged to self-destruct instead of killing people.
And then there's poor what's-his-name, turned into a death-headed servant of darkness. And Suman, who Allen gave so much, pointlessly, to drag back. And poor, poor, broken Alma Karma.
Ryuga wasn't really a Big Bad, but a rival to Mahoro. Difference is motivation. A better example of this is Minawa from the second season, who is The Mole until her turn She realizes she has a heart after she lured Mahoro to Management's fortress, using Suguru as bait. A heart (ability to have emotions) was the prize the real Big Bads dangled in front of her. She didn't realize she'd get one through The Power of Love, simply by staying with Mahoro and Suguru. She is then instrumental in freeing Mahoro from the trap she herself lured Mahoro into. This also catalyzes the end of the series, as it cuts Mahoro's life short, well short of the original deadline.
Actually it happens to everyone. Schneizel leaves Britannia and makes up his own rebel side after failing to murder the Emperor, the Black Knights join him, Gino joins the Black Knights, and Suzaku betrays Charles, though joining Lelouch could be considered a Heel Face Turn anyways. Because the definition of what each side is changes so drastically, the rest of the Rounds are harder to place: Betraying Britannia or staying loyal to their former boss? This being Geass this could be a Face-Heel Turn depending on how if you believe the new Britannian emperor is an antihero or an antivillain. Really after the betrayal there are no good side or bad side, just a bad side, and an even worse side.
InuYasha: Sesshoumaru went from a human-hating jerk who wanted to kill his own brother to a fiercely protective sibling and mentor after taking in an orphaned human girl. After he and Inuyasha end up protecting each others groups a few times, they finally throw in their lot together and fight the Big Bad as a united force.
Bad Bird in Samurai Pizza Cats who joins up with the good guys after a speech from Speedy saying that if Bad Bird helps Cheese win, everyone in Little Tokyo dies, including Bad Bird's girlfriend.
Rocket from Ginga Densetsu Weed starts off as one of Hougen's spies but after about 3 episodes, he becomes one of the nicest dogs in Weed's pack.
Adette Kistler from Overman King Gainer joins the Exodus once she is forced to stay in the city units for a while. She eventually even takes command of her own group of fighters.
Creed from Black Cat does this in the anime, though this was not present at all in the manga. Which makes it all the weirder why they decided to make him more perverted and depraved than in the manga.
In Claymore, Isley does this during the timeskip when he was living with Priscilla and Raki. Too bad the audience only finds out right before his death.
In Gundam 00, A-LAWS members Kati Mannequin and Patrick Colasour vanished after the Time Skip. Then they come back under the Katharon to help the Celestial Being attacking the A-LAWS, while reciting just how corrupted the A-LAWS is, the reason of their defection.
Fresh Pretty Cure! has Setsuna Higashi/Eas defecting from Labyrinth, undergoing a Disney Death, and in the process becoming Cure Passion, Fourth Ranger to the girls—all in episode 23. At the end of the series, her ex-comrades Westar and Soular join her on the side as good as well, also suffering a Disney Death when it happens.
Scar and Lust both have one in Fullmetal Alchemist; however, in both cases, Redemption Equals Death, as Scar is killed protecting the citizens of Lior, his last act being to save Alphonse, while Lust was killed by Wrath as she tried to help Edward save his brother.
Also, arguably, Wrath from the movie, Conqueror of Shambala, who leads Alphonse to Amestris Central City so he can open a portal to Earth, and also fights the other remaining homunculus besides himself, Gluttony. But again, Redemption Equals Death, since Wrath willingly sacrifices himself so Alphonse can open the portal, though he says himself all his wants to do is see his mother again in the afterlife. He gets to.
Zelgadis's two henchmen Zolf and Rodimus in the first season, as well as Rezo. Zelgadis is also established as a villain early on, but the Spoiler Opening notes his turn ahead of time.
Zangulus and Martina in the second season (they even end up together romantically!)
Duclis manages to come around by the end of the fourth, although he becomes more of The Atoner. The manga adaptation plays this straight, though. And due to his entirely different role in the novels, this never occurs there.
In Rave Master, this happens more often than not. Julius, Shuda, Let and Lazenby all making prompt turns after losing to Haru or others. Also notable are King, Jegan and Captain Hardner, who make Heel-Face Turns the exact moment before they die. And then there's the case of Reina, who makes a Heel Face Turn but then undergoes aHeroic Sacrifice afterwards.
Lupin III (Green Jacket) has Goemon, who provides one of the most downright efficient and drama-free turns ever. When first introduced, Goemon is an all-business samurai who has declared that he alone is worthy of killing Lupin. They duel a couple of times, each time ending in a stalemate. Their final confrontation ends with Lupin chasing Goemon in half a car. Realizing the absurdity of the entire situation, the two of them begin laughing and hugging like a couple of old drinking buddies. The episode ends there, and from the next episode on, Goemon is a dedicated member of Lupin's gang.
In Moon Phase, Elfriede breaks free from her servitude to her vampire father and joins the main cast in their hunt against the bad vampires whilst remaining a vampire herself.
Viral from Tengen Toppa Gurren Lagann goes from being the Decoy Protagonist's rival to being The Lancer. Lordgenome himself also "joins," but in this case it's just a bio-computer whose core is his disembodied head. He does later regain his full memory, though, and fights alongside the heroes in the final battle.
One Piece does this a lot. Nami, Robin, and Franky are Straw Hat members who were all initially portrayed as villains, or simply antagonistic to Luffy.
Nami did a double High Heel-Face Turn, posing as a pirate hating thief, while being a pirate, then joining Luffy after he kicked the crap out of Arlong.
Franky beat up Usopp before joining the crew, and if CP9 hadn't come into the picture and cut the Cycle of Revenge short, he may have never joined them.
Several villains experience this as well to varying degrees. Buggy, while still evil, became more caring for his crew after his defeat. Hatchan (one of Arlong's subordinates), Bon Clay, and Mister 3 (of Baroque Works) all showed up again much later to become an ally of the Straw Hats; even the arrogant leader of Baroque Works, Crocodile eventually allies himself to Luffy in his escape from Impel Down, and though dismissing it simply as something he's doing because his own convenience, he ends going out of his way to save Luffy from a certain death in the battle of Marineford. Notably, CP9 defects from the World Government after their defeat…but in all likelihood, they turned from Heels to Wild Cards.
Technically, there's even Vivi, who started off as a de facto Arc Villain before it was revealed that she was Good All Along.
Heck, a lot of the Straw Hat Pirates' friends are formed from Enemy Mine, Fire-Forged Friends, or Defeat Means Friendship: the Shandorians, the Franky Family and Galley-La Company, the Rosy Life Riders, the Kuja tribe, the prisoners of Impel Down, the Whitebeard Pirates, Neptune's Army, and most recently, Smoker, Tashigi, the almost Ax-Crazy Marines of G-5, and a pirate-hating samurai by name of Kin'emon (though he's far from the first pirate-hater that the Straw Hats befriended). Smoker and Tashigi already respected them because of the Alabasta incident; just how close they are now has yet to be revealed. But their subordinates? Much to Smoker's exasperation and Tashigi's amusement, they've stated that they'll start admiring the Straw Hats unless they act as if they're no different from other pirates.
Bleach is full of these. Perhaps the most notable is that in the final arc, Ginjo, Tsukishima and Giriko from the Fullbringer arc reappear in Soul Society, training with Kukaku and Ganju for the next Vandenreich invasion.
And the opposite. Also notable that several characters switch sides without altering their personal moralities at all.
Is a defining characteristic of Shaman King, particularly so in the manga. The Messianic hero converts all villains to his side, one after another, with his laidback attitude and genuine empathy for their motives. The heel face turn often is so through, it recast the character in a whole new light. Homicidal Chinese boy Tao Len is shown as a proud warrior with a sense of duty, while bully and delinquent Ryū is revealed to be a working-class champion and a road-travel hero.
This is all over the place in Kenichi: The Mightiest Disciple. Almost all the members of the Shinpaku Alliance were originally Kenichi's enemies at some point.
This is a Defeat Means Friendship show. Mostly. Exceptions are made for particularly impressive psychos and the lead, who does not betray his principles when defeated. Which is good, because he loses enough early on that it would have become a fascinatingly schizophrenic series if he had.
That actually sounds kind of cool. You could set it up a little like JoJo's.
In Rosario + Vampire, every girl in Tsukune's Harem, other than Moka (and possibly Yukari, who initially behaved more like a Screwy Squirrel than anything), started out trying to kill, control or abuse him. As did their club president, Gin.
In Outlaw Star, the evil Anten Seven's leader Hazanko sends elite assassin Shimi (a.k.a Leilong) to eliminate Gene Starwind when he is considered a threat to his plans. Gene faces a much weaker assassin and impostor of the real Shimi but barely wins. The real assassin converses with Gene in a bar as Leilong and you can tell he is thinking about making a serious change in his life while not revealing his true identity as an assassin to Gene. Later on, Leilong engages in a Curb-Stomp Battle against Gene and his crew. Gene the last one standing of his crew agrees to a gun duel to the death which has Leilong get "killed" because of his faulty gun. Turns out the whole battle was orchestrated by the assassin to fake his own death, and to leave the Anten Seven. Word of God states that Shimi was actually a Dragon and his power was SECOND to Hazanko's level, so if Shimi didn't have that Heel Face Turn the Outlaw Star crew (who were much weaker at the time) would have been killed off before the hunt for the Galactic Leyline.
In Nabarino Ou, just about all of the main "bad" characters introduced early on end up teaming up with the good guys in the end to defeat Fuuma. Though most switch sides much earlier on.
A Certain Magical Index is partial built on this trope, as one of the themes of the story is that there are no bad guys in the conventional sense. In order of appearance they are:
Accelerator, who then goes on to become the secondary protagonist of the series.
Agnese Sanctis and the Agnese Forces. Though it could be argued that it was a change of situation, rather than a change of heart.
Hamazura Shiage, who then goes on to become the tertiary protagonist of the series.
In the original English language manga Amazing Agent Luna, Timothy Hyatt, upon learning Elizabeth Westbrook is to be killed, switches sides and helps her escape. He later returns to deal with his former partner, Martin Williams.
It is unclear when Yuri Nakamura in Angel Beats! made the turn, but there are two very likely candidates. The first is in episode 11 when she orders the SSS to put some serious thought into passing on before the Shadows overtake them like they did Takamatsu. If that doesn't seal the deal, then the climax of episode 12, where she blows those computers to hell that were responsible for the Shadows in the first place definitely does.
Kanade Tachibana goes from Type IV Anti-Villain to Woobie very quickly after being deposed from the Student Council. Her subsequent reinstatement at the end of episode 9 can be seen as a Heel-Face Revolving Door, but Yuri quickly starts agreeing with her after one of her own boys gets taken down by the mysterious and malevolent Shadows.
Several characters in Pokémon Special, namely: Sabrina, Koga, Lt. Surge, Blaine and Mewtwo, the Kanto Elite Four (save for Agatha), Will and Karen, Pryce, Courtney, Tabitha, Amber, Deoxys, Cyrus and all the Team Galactic commanders (except for Charon.)
Magic Knight Rayearth has a quite few of these, the number of which depending on whether you saw the manga or anime. In the manga and anime, Ascot, Caldina, and Lafarga, who all served Zagato in the first storyline for various reasons (wanting somewhere to belong, money, and mind control, respectively), all do a Heel Face Turn thanks to the Magic Knights. The anime also adds Alcione, Eagle Vision, and Nova to this list. Lantis could probably also be considered a more subtle version of this trope.
YuYu Hakusho has several of these throughout the series, including (in order of side-changing) Kurama (kinda; he wasn't really evil anyway, at least not within the show's scope), Hiei, Rinku, Chuu, Touya, Jin, Suzuka, Shishiwakamaru (once retconned into surviving his battle with Genkai), and Seaman/Kyoshi Matarai.
Plus Yusuke himself, kinda, at the very start. And Yomi, sort of, toward the end.
In Negima!, Kotaro underwent one of these after the Kyoto arc. More recently, Shiori/Luna seems to be on Negi's side now, although Ala Alba is still certainly suspicious of her. Though now that Fate survived the attempted door slam on his own Heel Face Turn, it's assumed that all of Fate's pactio partners including Shiori have officially switched sides as well.
Trinity Blood has several examples Abel and Tres do this in their backstories. Then is Radu (who has a Heel Realization) in The Iblis ending. Surprisingly Dietrich in the Stories Untold.
In Tenshi Ni Narumon Mikael, after acting like a nice guy for the majority of the series and then turning into an evil and insane twit, does exactly this. Yes, the boy has issues.
Tsubasa Reservoir Chronicle seems to love this trope. The most noticiable example is Fai, who is revealed to have been working for Fei Wong, but has a change of heart following the events of the Acid Tokyo and Infinity arcs. Xing Huo might count as another example, as she eventually betrays Fei Wong by helping the real Syaoran to escape, and the clone Syaoran also undergoes this transformation durring the Final Battle with Fei Wong. Although, one might say that Fai's was a bit more sucessful than the latter two's...
In an inversion of the Moral Event Horizon trope, Haruhi Suzumiya becomes moresympathetic toward the end of the second light novel, Sigh, as well as its anime adaptation following a close brush with Kyon's fist for not only spiking Mikuru's drink and leaving her open to possible rape but also calling her her toy.
Zatch Bell! has several of these: Pamoon, Penny (Patie), and Byonko in the Ancient Mamodo arc; Purio (Papipurio), Rodeux and Zeno (Zeon) in the Faudo arc; and Gorm (Goomu) in the King's Festival arc. Unfortunately, Redemption Equals Death (or returning to the Mamodo/Demon World) for all of the above examples except Purio (and Zeno, who was "dying" just as his Heel-Face Turn was finalized).
There's also Zeno's partner, the psychic genius Dufort (Dufoux); sold to a mad scientist by his mother at a young age, he met Zeno immediately after he was left to die. The hatred he had ran deep, but thanks to the true power of Zatch's (Gash's) Bao Zakeruga spell, it dissolves, and he becomes a crucial ally in defeating the final Big Bad.
Ryoko in Tenchi Muyo! especially the TV Alternate Reality of Tenchi Universe who starts out as a space pirate (Along with Hakubi Washu) who reforms upon falling in love with Tenchi. In the original OVA it turns out she was under a type of mind control.
Zero fills the trope much better in the OVA after uhhhhh ... she? betrays Dr Clay because she refuses to follow his orders to kill Tenchi. She later merges with Ryoko.
Sasame in Prétear after his earlier Face-Heel Turn is seen in the end happily living with Takako. Takako also decides she's had enough and switches sides in the end, it doesn't help much because she's still used by the Big Bad Tree of Fenrir but can't hate her for trying.
Subverted in the Soul Eater manga — Crona had changed sides, but comes back to the dark side at Medusa's request. And to make things worse, Crona kills Medusa and now goes on collecting the Kishin eggs. The face turn sticks in the anime.
To a lesser extent, Black Star. He's not really a villain, but he's an arrogant son of a bitch only looking out for himself and generally willing to injure anyone in his way to prove he is the "strongest", even once threatening to his own friend, Maka, that he would beat her up. Later, he becomes more caring towards others and more noble.
In Arata Kangatari, this is, so far, what essentially happens for any Shou who unites under Hinohara's cause, whether it be through joining his travelling group or submitting to him and his hayagami.
Hiyori from Kotoura-san does one after episode 4, when she realized she caused a lot of trouble for Manabe and didn't understand how much pain Haruka was trying to hold in.