Miles Edgeworth of the Ace Attorney series. Edgeworth was raised by his foster father Manfred Von Karma after his real father Gregory Edgeworth was murdered. Miles became obsessed with proving defendants guilty convinced that he needs to be perfect. Manfred Von Karma turns out to be the murderer and allowing Edgeworth to reconsider his perfectionist record and the Turn is complete in Justice For All.
In Baldur's Gate II: Throne of Bhaal, you can resurrect Sarevok, the Big Bad from the first game, and have him join your team. This is also what happens in the book adaptation. He is still evil, though, but that can be changed (all the way to good) if you make the right choices (he partially falls again, per his epilogue, torn between his old Chaotic Evil self and his new Chaotic Good self in his actions).
Leliana in Dragon Age: Origins. At the start of the DLC Leliana's Song, she is a thief, a troublemaker, and a murderer. Once she is betrayed by her mentor and lover, and escapes from prison after being tortured, the Chantry takes her in. She becomes the pious bard in the main game, and is the most pure good aligned member on the team.
Zevran starts off as an assassin who tries to kill the Warden, but depending on the player's choices, can wind up being part of the team.
Shepard has a similar effect on Jack, who goes from being an Axe Crazy murderer and criminal, to a reformed, genuinely beloved Badass Teacher at Grissom Academy, helping biotic children hone their powers. The Citadel DLC reveals she also rescued a biotic Varren from an animal shelter and helped it overcome it's past mistreatment, though she apparently doesn't realise the obvious parallels to herself.
Mass Effect 3: In two of the game's four endings, this trope is used on the Reapers. In the Control Ending, Shepard becomes the new leader of the Reapers and promises to rebuild the galaxy and protect its people. In the Synthesis Ending, Shepard triggers a galaxy-wide event that transformers all life into a new form of synthetic-organic life. The Reapers help the galactic races rebuild their homes, sharing the wisdom of the civilizations they harvested in the past.
Paragon Shepard and Nyreen are able to push Aria T'Loak further into Jerk with a Heart of Gold territory over the course of the Omega DLC, convincing her of better ways to retake the station instead of sacrifice innocent lives. This eventually seems to reach her and at the end, she declares to the masses that "Weare Omega" and appears amazed when she realises they are cheering for her out of adoration, not fear.
In Chrono Trigger, it is possible to talk the villain Magus into joining your party. This is represented less as a change of heart on his end than as a realization that he could achieve his goals by working with the heroes. By the time the option to have him join comes about, his intent and motivation have been revealed, perhaps making him more of an Anti-Villain. On the other hand, when he becomes a party member he appears to become somewhat less of a sociopath.
To be fair, though, you do not know that he was a sociopath. He was just the ruler of a country/army/something, that just happened to oppose the humans. But in war there are no sides. Ultimately it seems like he was just doing what was necessary. In fact, the first thing he does after joining the party is telling you how to bring Crono back to life, despite having no self-serving reasons for doing so. He does this even if you decide to fight and kill him, meaning that no change of heart was involved; he was never truly evil to start with.
In its sequel, Chrono Cross, many characters you can eventually play are former bosses. One will even apologize for fighting you earlier in the game.
Also, Cammy, though this is a case of being cured of Bison's Mind Control rather than choosing to switch sides. After being cured, she joins the British government in order to bring him down.
Star Gladiator's Zelkin Fiskekrogen had started out as a member of Dr. Edward Bilstein's Fourth Empire, hoping to get revenge against Earth and the humans for a past war that had occurred between them and his home planet of Klondike. However, after fighting against Hayato Kanzaki and realizing that not all humans were bad (not to mention having to also realize that Bilstein was far worse than the humans), Zelkin had defected from the Fourth Empire and joined up with Hayato and his friends, determined to set things right while atoning for his past crimes.
Aside from Zelkin, Blood Barbarians was also a member of the Fourth Empire as well (albeit when was Brainwashed and Crazy) and upon having to break free from Bilstein's brainwashing, Blood was also determined to set things right while atoning for his own past crimes, joining up with Hayato and the rest of the Star Gladiators.
In Advance Wars: Dual Strike, Hawke and Lash come to the Allied Nations' aid after being saved by them.
Tasha and Gage reluctantly join the Rubinelle Army in Advance Wars: Days of Ruin following the death of their original commander, Forsythe, when Will decides not to kill them.
Alma from the Xbox remake of Ninja Gaiden fights Ryu twice, proving to be a difficult foe both times. However, when Doku, The Dragon, attempts to sacrifice Alma's twin sister Rachel, Alma has a change of heart and throws herself in the way of Doku's blade.
The good character Faust from Guilty Gear X onward is incredibly strongly implied to be the villainous character Dr. Baldhead from the first game in the series, after undergoing a Heel Face Turn and taking a new identity.
The Arbiter in Halo 2 initially works against the humans to atone himself in the eyes of the Covenant Prophets. When the AI 343 Guilty Spark reveals to him the truth about the Great Journey they want to bring about, namely that it will destroy all life on a galactic scale, he reluctantly sides with the humans.
By the end of the trilogy, though, he's an eager ally. The rest of the Elites...eh, not so much.
Avernum 4 has Rentar-Ihrno at the very end of the game, if you make the right dialogue choices.
Lakilester in the original Paper Mario. When you first meet him he's working for the current chapter's boss, but after a quick battle and a love scene he decides to join you.
Shiro Amakusa Tokisada from Samurai Shodown turns into a good spirit in Samurai Shodown IV.
Magnus Armstrong, one of the antagonists from No One Lives Forever is convinced to join the good guys in the sequel, No One Lives Forever: A Spy In H.A.R.M.'s Way.
Happens all the time in Super Robot Wars, if a character has the least bit of sympathy he will usually do a Heel Face Turn. This is so common that in Original Generation 2 they start lampshading it by mentioning that they can expect a recent convert by mentioning all the other people who have done it.
In Destiny, some could only join if they were convinced Glacies, Wintos, Margue, Chronicle, Katajina, Roze, Gabil. Haman Karn of all people can join you if Judau, Char, and Camille rack up an obscene number of kills. It's nearly impossible on your first playthrough, but New Game+ all but assures it on later runs.
While it is very common in OG, the one most notable and most impressive Heel Face Turn would be the one pulled by Axel Almer in OG Gaiden. He doesn't just do normal defection like the others, he shows his Heel Face Turn by saving a Brainwashed and Crazy Lamia, who was once thought to be dead and was now about to die again and sticking a metaphorical knife to the team for failing to save her again. So awesome that this scene becomes Axel's definitive Crowning Moment of Awesome, and also counts as a Crowning Moment of Heartwarming as he lets go of his hatred for Artificial Human in general, and while he doesn't officially join the group, he has forever earned the trust of the heroes as a good guy.
In Guild Wars: Nightfall General Morgahn is one of Varesh Ossa's generals and quite devoted to his religion, and tolerant of Varesh's. While he appears to be a villain who is not actually evil, just loyal, he actually makes a heel-face-turn and joins the player character, and being required to face Varesh Ossa.
In Super Smash Bros. Brawl The Ancient Minister is thought to be the remorseless leader of the Subspace Army, but actually regrets his actions. In truth he isn't the true mastermind, and thus lost control of of his R.O.B. Squad when Ganondorf stepped in to complete the job of destroying the world with Subspace Bombs. The Ancient Minister then interferes, only to be attacked. It is then his true form is revealed, a R.O.B. From there is only referred to as such and becomes playable.
To be fair, the villains in the Subspace Emissary mode who are also playable characters do join up to fight the last boss. It doesn't help that the Big Bad pulled a 'You are of no more use to me' on them all.
In a case of All There in the Manual, it is revealed that Mr. Game & Watch is actually a villain, until Peach gives him her parasol. He was apparently not really evil, just incapable of telling the difference between good and evil. Hence, the ease of his turn.
We've replaced Sparda's unbidden evil with Folger's Crystals. Let's see if he notices...
Raiden, a cruel, gigantic wrestler from the Fatal Fury series of fighting games (and Capcom vs. SNK 2), eventually underwent a literal Heel Face Turn, taking off his mask and becoming the benevolent Big Bear. The fact that wrestling is fake has become a little too real for him
Similarly, 3 Count Bout features one of Raiden's old rivals, the vicious heel Big Bomberder, working a face gimmick by donning a mask to become Gochack Bigbomb. In this case, it isn't a sincere character shift — it's Big trying to get over with the fanbase (and not doing so hot).
This one is a Heel-Face Revolving Door of sorts, because Beat starts as a player, becomes a Reaper and a villain, but then performs the Heel Face Turn for the last Game.
After defeating Zidane and friends three times in Final Fantasy IX and getting a Pyrrhic Victory after the third battle upon realizing Garnet's condition, General Beatrix joins your party for a couple of fights and seeks to atone for what she has done.
An unusual, less extreme example, but it counts. Steiner, even though he's in your party for a greater portion of the game, spends most of his time trying to sabotage the party and deliver Dagger back to the queen. Zidane and the others win his loyalty, eventually.
Even Big Bad Kuja pulls this off before he dies at the end of the game. Just when Zidane comes to pull off a Heroic BSOD to pick him up just as the Iifa Tree is about to crumble.
Happens in every Fire Emblem game, sometimes more frequently than others. Usually you have to talk to the recruitable enemy with a certain character, but sometimes a former villain will automatically join your side. Binding Blade had Miledy and Douglas, Sword of Flame had Heath and Vaida, The Sacred Stones had Duessel and Amelia, and Path of Radiance had Jill, Muarim, and Ena. Additionally, Awakening gives you the option of recruiting two former villains, Gangrel and Aversa.
In the Persona 2 games, this happens quite a bit, although most of them don't end up joining the party, just being good guys instead of bad guys. In Innocent Sin, Jun does this after breaking free of Nyarlathotep's influence. As well, Principal Hannya would either die or end up pulling a Heel Face Turn depending on a rumor the protagonist ended up starting with a throwaway dialogue choice. Finally, depending on choices, Anna Yoshizaka would either pull a Heel Face Turn or be replaced by a Shadow counterpart created by Nyarlathotep. In Eternal Punishment, many of the previous villains were forced into Heel Face Turns as part of making a Merged Reality; however, Tatsuya Sudou was so deranged and irredeemable that he was instead imprisoned in a mental institution... and Ginji's Heel Face Turn doesn't end up sticking as he is pulled back into essentially the same role he played the first time around.
Judith Mossman in Half-Life 2. At first she seems to be one of the good guys, but then it is revealed that she is actually working for Dr. Breen. At the end, she pulls a Heel Face Turn and betrays Breen.
Also the Vortigaunts in the series itself can be interpreted as a Heel Face Turn. They go from attacking the player in the first game to worshipping him in the second, though it is because Gordon freed them of the influence of the Nihilanth (but that may not be something the player expects to know right away).
Klungo in Banjo-Tooie, after he realizes battling with Banjo and Kazooie is making him less and less handsome, and now Mrs. Klungo won't want him anymore!
Even final bosses can get into this. In the DS remake of Dragon Quest IV, a 6th chapter is added in which allows you to revive Rose, and use The Power of Love to convince Psaro the Manslayer (the aforementioned final boss) to not only stop his plans for world domination/destruction, but also to join your team! His Evil Chancellor then takes over the main villain position.
More an Enemy Mine situation. The Knights have no interest in being heroes, or even being liked (most death knight NPCs, in fact, have quest and gossip text that can be summed up to "Are you useful? If so, good, I've got work for you. If not, piss off."). Their sole motivation for allying with the Argent Crusade is to see the Lich King's head on a pike.
Deus Ex has Daedalus, an AI programmed by MJ12 to hunt down terrorist groups who might threaten their regime. Unfortunately for them, when the AI examined his creators and their actions, he classified them as a terrorist organisation themselves and left to help the player bring them down.
Saki from the Oneechanbara series. Initially the villain, she's revealed to have a pretty good excuse.. and kidnapped by Eva. After Aya rescues her, she stops trying to kill Aya and joins her.
Meliadoul in Final Fantasy Tactics (too bad this happens after Orlandu's already joined, however; everything she can do, he can do better). Also, Mediators can use their Invite skill on most enemies (as in, those who aren't plot characters), recruiting them on the spot to your cause (well, with a bit of luck, anyway).
Darth Vader's secret apprentice in The Force Unleashed. Although the fact that he just found out that his entire life was based around the fact Vader wasn't using him to help kill the Emperor but, rather, bring those who would speak against the Emperor out into the light probably helped a lot.
Jin Kisaragi from BlazBlue is an unrepentant Class S Asshole, mostly due to his extreme possessive attitude that he wants to make Ragna his and his only and hates his little sister Saya for that. However, after turning into Hakumen, he becomes a much better person who doesn't obsess on his brother and has never mentioned his little sister again; and also became one of the Six Heroes, saving humanity. In fact, Hakumen himself feels really disgusted at the depravities he caused as Jin, and now all his fights are his way to atone for his sins.
Byrne from The Legend of Zelda: Spirit Tracks, after Anjean, Link and Zelda nurse him back to health, despite everything he did to them. He also received a harsh beating from the guy he helped revive before that.
In Ocarina of Time, Ingo the spiteful ranch hand later becomes Ganondorf's minion and takes over the ranch. He kicks Talon out and makes people pay to visit. He mysteriously changes his ways after you escape with Eponanote It's implied that Ganondorf [[You Have Outlived Your Usefulness just leaves him.
Bomb-Master Cannon from The Wind Waker overcharges prices for bombs until Tetra'sPirate Crew steals them. Afterwards, he realizes he could lose his business if he doesn't start selling his bombs at reasonable prices and people resort to stealing, so he sells his bombs at a much more reasonable price.
Chudley/Malver from Twilight Princess sells items at ridiculously high pricesnote The cheapest of which is 10 arrows for 2000 rupees. until Malo buys out his store. After which, he becomes nice and will actually warn Link if he's wasting his money.
Groose from Skyward Sword goes from being the jerk of the town who hates Link and constantly bullies him (he even hides Link's Sacred Loftwing so he can't win the big race), to actually respecting and helping Link near the end of the game. For example he builds the "Groosenator", a huge catapult, that helps you in the final Imprisoned fight, and he even turns up for a Big Damn Heroes moment during the second to final fight agasint Ghirahim when he turns up just in time to save Zelda from falling to her death.
There are many characters in the Suikoden series that join you this way.
A good example comes from Suikoden I: All but two of the Great Generals will join you if you opt to show them mercy rather than have them executed. The only two who don't join you are your father, and Ayn, both of whom die at your hands. The Generals who do join you are required for the best ending, in which Gremio is resurrected.
The plot of No More Heroes 2: Desperate Struggle is centered around TravisTouchdown gradually turning from a mostly remorseless killing machine into a better person. Although a point can be made that he treads the line between heel and face during the course of the first game and a good portion of the sequel too. Indeed, if he weren't a merciless assassin, this would almost be a case of Neutral No Longer, due to his attitude during most of the series.
And then there's one of the ranked assassins, Shinobu, whom Travis spared, who becomes his ally and self-proclaimed apprentice.
In Fallout 3, you can convince President Eden to do this. Though Colonel Autumn has gone against the president and ordered his men to attack you on sight, President Eden counters by having all the Sentry Guns and Security Turrets attack the Soldiers so you can get away easier.
In Final Fantasy VI, Celes betrays the Empire, and joins the Returners after Locke saves her from torture. Kefka's plan to poison the entire town of Doma crosses her Moral Event Horizon. However, burning down Maranda is simply Empire evil, because she did participate in that.
Ruecian also makes one in Threads of Fate with Rue's story.When Valen binds Rue with a doll binding magic Ruecian casts a spell that unleashes Rue's true power, but ends up killed by Valen that also counts as Heroic Sacrifice.
The Disgaea series is full of these kind of characters, though what exactly is a heel face turn and what is instead a Face-Heel Turn can be confusing given disgaea's peculiar brand of Blue and Orange Morality. In fact, the first and third Disgaea games are mostly ABOUT the gradual change from villain to anti-hero.
Gold Knuckle in Disgaea 3 refers to his side change as "turning face!".
Rogue Squadron: Kasan Moore, head of the 128th TIE Interceptor Squadron, defects to the Alliance and provides valuable information. She was from Alderaan, so yeah.
The Orcish Horde from the Warcraft video game series. In the first two games the orcs were Always Chaotic Evil, their leaders having sold them into the service of the demonic Burning Legion. But prior to the start of Warcraft III the orcs, under the guidance of their new warchief Thrall, rediscovered their ancient traditions and the concept of honor, and became a Proud Warrior Race Guy society.
This gets escalated even moreso in the MMO ''World of Warcraft, where the entire Horde not only becomes playable, but is seen as also fighting for similar goals that their enemies the Alliance wants. In fact, the main enemy itself ends up shifting from the Orcs to different people (Old Gods, Deathwing, The Lich King).
GLaDOS, from Portal 2, after being put in a potato and spending the middle to the end of the game with your character. She then becomes very nice to you, then is reset back to disliking you, but is still good enough to just want you gone instead of dead.
The General, from Mega Man X4, returns to the course of duty after the death of the Big Bad, claiming that Sigma had "blinded him to the truth", which may or may not have implied brainwashing. Probably not, considering that at the beginning of the game, he ignored him until the Sky Lagoon's crash forced his hand.
Uruka, Kouin and Kyouko in Eien no Aselia all start out on various enemy sides. The first is kicked out and nursed to health when she loses the ability to fight and the latter two switch after the mind control over Kyouko is broken.
Three of the Fake Evil Kings ( Big Bull, Linda, and Epros) in Okage: Shadow King end up joining you after being defeated.
Septerra Core. Araym; Selina twice; Lobo, years before he meets our heroes; in-game mythology ascribes one to Dogo, god of mischief, who helped save the world. Doskias does one in the ending, but alas, Redemption Equals Death.
The Kuvasz Guild of Solatorobo, after Opéra takes over due to the death of Bruno.
Judge Gabranth in Final Fantasy XII sides with The Empire after believing that his brother, Basch, betrayed them and his men. He even fights the party a few times but near the Final Battle, he realizes who the true evil is and assists the party for one battle. Gabranth dies after the war is over and Basch lives on in his name.
Matt Miller, leader of the Deckers in The Third, joins the Saints in Saints Row IV.
In the final two routes of Duel Savior Destiny, Imnity switches sides out of concern for the life of her master, who is not really on the same side as her. Nobody comments on the whole 'she was just trying to end the world' thing either.
Magolor from Kirbys Return To Dreamland. After Kirby and his friends defeat Landia, Magolor steals the Master Crown and goes off to take over the universe. He is defeated, but in the next game, Kirby's Dream Collection: Special Edition, he has reformed and made an amusement park for Kirby.
Tatjana from Arc the Lad: Twilight of the Spirits. However, she proves to be an interesting case - in a lot of these cases, the person who does this becomes completely good - but Tatjana still retains her old personality. She never shows remorse for the things she had done to Camilla or other Deimos.
After being maimed and disfigured by Outworld warriors in Mortal Kombat 3, Kabal renounces the vile Black Dragon organization and becomes a crimefighter at tournament's end- - only to pull a Face-Heel Turnthree games later when he's unable to shed his thuggish past.
BioForge: Caynan, one of the Mondite guards. Unfortunately, it didn't turn out well for him and he was made into a test subject himself.
Near the climax of Emerald City Confidential, Cutter, who was working with the Big Bad, suddenly has a Heel-Face Turn when he accesses the magical powers of the Spirit Rod and learns the truth about his past. Specifically, he realizes that the protagonist is his older sister, who has been trying to find him ever since he went missing as a baby. This leads to him working with her to defeat the Big Bad.