City of Heroes Going Rogue allowed you to live this trope. You can go from being a hero to a villain back into a Hero, wash rinse repeat. Ditto villains.
The Rogue's Gallery enemy group consists of Heel Face Revolving Door consists of former members of the Paragon Heroes and Rogue Isles Villains enemies from Bank Missions with fleshed-out personalities, as well as several prominent NPCs like Frostfire and Malestrom. Many of these NPCs undergo alignment changes just like you do. Frostfire becomes a Hero, Polar Shift becomes a villain... But as the missions are random, it appears as if they're hopping all over the place, Just like you.
Metal Gear Solid 4: Guns of the Patriots: Oh, Naomi, do you even have a side? From the beginning to the end of the story, she helps Snake, betrays Snake, helps Otacon, sleeps with Otacon, betrays Otacon, then helps Snake and Otacon. And then leaves one last message for Otacon and Snake after she dies for good measure.
Theoretically you can take a spin in the Heel Face Revolving Door in just about any RPG with a morality system. Just alternate good choices and evil choices and voila.
Kain of Final Fantasy IV is pretty often used as an example, though all his turns were due to mind control by the real villain.note It's still discussed if his first Heel–Face Turn was an act or the real deal, and he gets controlled again later. And it happened only twice. So, mainly it's a case of Never Live It Down.
Lampshaded in the DS remake - if you use the "read the party leader's thoughts" feature (set Kain as the visible character on the map, then bring up the menu) as you're leaving the Sealed Cave, you'll see him fighting Golbez reasserting control (unsuccessfully). If you repeat this as you travel through the Lunar Subterraine, Kain will be fighting the attempts of Zemus to control him (this time more successfully).
Subverted in the sequel, where Kain joins forces with the villain the Mysterious Girl, he steals several crystals and fights Fabul before being defeated by the Hooded Man who is Kain: the evil Kain is actually his Dark Side, who escaped Mt. Ordeals. The real Kain had to track him down before being able to pass his test.
Captain SNES: The Game Masta of course uses the trope again, as not only he is touched by the sovereign of sorrow, he is also in love with Rosa (pretty canonically) which the Drab Lord amplified sufficiently as to make him his minion. Kain is referred to here in Dungeons & Dragons terms as "the reason you don't make Charisma your Dump Stat", and its implied that he will fall for any charm person spell. Any.
Aribeth jumps around quite a lot in BioWare's first Neverwinter Nights. To date it is possible to have her switch sides five times.
Betraying Neverwinter to Morag, being redeemed in the endgame, going mad in hell, being brought back by the player, and falling to Mephistopheles' "Reason You Suck" Speech. Then again, all of the others technically stem from the first one, so if you don't take either player-prompted switches she changes sides once and stays there.
Taken on full throttle in Super Robot Wars Alpha 3 if you pick Selena Recital as the protagonist, where she's initially acting on her own (and fighting Viletta Vadim over a case of mistaken identity), shortly thereafter joins the Alpha Numbers, sides with ZAFT after a time-skip where everyone goes their own way, and falls back in line with the Alpha Numbers near the tail end of her introductory stages.
Char/Quatro still has the unfortunate habit of switching sides in the Z series and coming back if the conditions are right. He sides with the other half of ZEUTH (Z1), the A-LAWS (Z2: Saisei-Hen), and then Neo Zeon (Z3: Jigoku-Hen).
Strangely enough it's a bit of a subversion in Z3. As it was more of a case of Superdickery on Char's part to get the heroes against Neo Zeron and to prevent them from dropping Axis. After that he joins the heroes again, presumably for good this time.
Heero Yuy works for Char Aznable in Shin Super Robot Wars at first because he rescued Heero from a harsh life at the hands of the Zanscare Empire. Later on, General Oka gives Heero new orders from Doctor J to stop Char himself. However, he couldn't follow these new orders until he discovers Char siding with the aliens. Heero tersely teams up with the Londo Bell and can join them as a Secret Character.
Lee from Tekken, who is introduced as a boss character working for Mishima. He's probably neutral to evil at this point; he is not as evil as Kazuya or Heihachi, but he's not shown to be good. Later on he becomes estranged from his family due to what Heihachi does to Kazuya at the end of Tekken 2. He decides he cannot work for someone who would do such things and so he travels the world, becomes a ladies man and eventually becomes a main character in his own right in Tekken 4, before becoming one of the best characters in Tekken 5 and onwards.
Heihachi sort of goes through this, more of a Heel-Villain Protagonist Revolving Door than anything else.
In Shadow the Hedgehog, Shadow can go from wiping out a platoon of GUN soldiers in one stage, blasting through the Black Arms in the next, then destroying Eggman's robots afterwards. Speaking of Eggman, the good doctor can be of either the "Hero" or "Dark" alignments in any given stage in which he participates. Which way he leans depends on who he's fighting against in that particular stage: he'll be of the "Dark" alignment if he's facing off against GUN, and the "Hero" alignment if he's fighting the Black Arms.
Depending on your point of view, this can happen to a lot of characters in World of Warcraft, especially if they're a member of the opposing faction. For example, King Varian Wrynn is almost universally loathed by the Horde, but the extraordinary amount of Enemy Mine in the game means that much of what he does is good for the Horde as well (like killing Onyxia), and he has his Pet the Dog moment in Icecrown Citadel. Similar arguments could be made about Horde leaders from the Alliance perspective.
The Orc race is collectively like this. They started as warlike-yet-honorable savages living in relative balance with the other races of Draenor. Then they drank demon blood and became complete monsters, with countless stories of slaughtered children and mass rape. After they were defeated by the Alliance the blood rage wore off, and after some time in concentration camps Thrall took them to Kalimdor and attempted to build a new nation that cooperated with its neighbors. The last chieftain who had drunk demon blood died killing said demon, bringing it all full circle. Now tensions have been rising with the Alliance, world war has basically been declared, and a large faction has gained power in the Horde in favor of re-militarizing led by a young idiot who has argued in favor of child-killing to a veteran who actually did it and was explaining that he was still haunted by their screams.
If you think about the Forsaken Death Knights, they own this trope. Initially they started out as humans in the Alliance, got killed and raised to serve the Scourge, broke free of the Scourge and joined the Horde, then died again and rejoined the Scourge only to break free once more and rejoin the Horde. It's incredible they can keep their sides straight.
Bowser in the Super Mario Bros. franchise, especially in the RPGs. He's been an Enemy Mine so often—to say nothing of when he Goes Karting With Mario—that it's hard to say just whose side he's on anymore. Although, in the RPGs at least, he only stays with Mario until the Big Bad is gone. Bowser himself often cites Evil Versus Oblivion when teaming up with Mario; he wants to rule the Mushroom Kingdom, whereas the Big Bads want to destroy it. Depending on the game, it's hard to tell how much of that is an act and how much is sincere.
Birdo, too, which has made her infamous along with her Transsexuality. In games where she's non-playable, she's almost always a boss, but in games like Mario Party, she's doing things like helping Mario defeat Bowser. And to add to the Mind Screw she's implied to be dating Yoshi.
Persona 3: Chidori starts off as a member of Strega, the crazy-end-of-the-world guys. She then quite inadvertently befriends Junpei, a member for the heroic SEES, who talks too much about what he does. She captures him and holds him for ransom essentially, but is then captured by SEES. Junpei works up a friendship with her to the point that she won't talk to anyone else, resulting in a Heel–Face Turn. Then SEES supposedly kills the other members for Strega, and she rejects Junpei. About a month later, she attacks SEES for a Face–Heel Turn. Five minutes later, she sacrifices herself to save Junpei, for a Heel–Face Turn, because of course Redemption Equals Death.
Captain Qwark of Ratchet & Clank. Initially, he was a hero, albeit a loud and boisterous one. Then, he became a villainous has-been. Then, he got his shot at being the Big Bad. Then, he changed his mind ans went back to being a boisterous hero. While he's treated as the Butt-Monkey and The Friend Nobody Likes among the good guys, he's been a hero consistently since the series made the jump to the PlayStation 3 and beyond.
The Kirby games love this trope, although it's much lighter than most other interpretations. Characters like Chef Kawasaki and Knuckle Joe can appear as mini-bosses in one game, and be allies in a different one.
While King Dedede is the perhaps the most obvious culprit of this, Meta Knight does this a staggering number of times in the very first game he was featured in. Most of the time, he's sending his mooks after you to impede your progress, and eventually directly confronts you himself. However, he also gives you invincible candy periodically throughout the game, even after you defeat him.
Fire Emblem Tellius: If you do things a certain way, Jill can change sides five times across the two games she's in (Path of Radiance and Radiant Dawn). That's one more than Kain up there!
That goes double for Naesala, who seems to have this as a basic character trait. Just in the first game he works for Daein, sells a childhood friend to a Begnion noble, if you manage to talk to him in one chapter (almost a must, as he's near impossible to kill) he decides to go neutral, then he somewhat grudgingly starts helping Crimea toward the end. The second game sees him helping the Laguz Alliance, selling them out to Begnion, and then acting as a bodyguard for the Apostle when she goes to support the Laguz Alliance! No one is quite sure what side, if any, he's really on by the time he's a playable character and more than one doesn't really care as long as they get to kill him. Lampshaded in Radiant Dawn by Tibarn, of all people.
Justified; Naesala is under a Blood Pact. If he doesn't betray everyone at the will of the Begnion Senate, all of the ravens will die.
Fire Emblem Elibe: Erik, a minor character changes sides throughout both games. First in the backstory of Blazing Sword, Erik was a friend of Eliwood, and Hector, but his jealously led to him joining with his father in turning against Lycia. Then after his father abandons him, Erik feels remorse over his actions, and cleans up his act as his father's successor. By Binding Blade, Erik, despite people's trust, in him joins up with the invading Bern Empire out of the belief Lycia has no chance of opposing Bern.
In Pokémon Mystery Dungeon Explorers of Sky, Dusknoir is a perfect example of this. After being sent back to the future with Grovyle, he finds out that Primal Dialga is now trying to get rid of him, and has a new henchman at its side. Due to this, he has to team up with Grovyle as they make their way to Primal Dialga. Towards the end of the episode when Grovyle attempts to rescue Celebi, he is captured in a trap set by Dusknoir that is designed to destroy Grovyle's soul so that Dusknoir can take over his body and go back to the past to foil the hero's plan to save the future. However, after remembering what Grovyle had told him about himself earlier, Dusknoir has a brief personality crisis before swiftly becoming a good guy and saving Grovyle at the last second.
Pretty Bomber from the Bomberman games. While originally a member of the Five Bad Bombers, she just can't make up her mind.
Ultimate Spider-Man has Silver Sable going from attacking Peter now that she knows he's the titular hero to helping him save the innocents to attacking him again to finally letting him go after Trask.
Vincent from Silent Hill 3 goes from sided with Claudia and Heather all over again until it's revealed he is neither sided with them as he, being an arrogant jerk, plans on having Heather and Claudia kill each other to save his skin.
Goro in Mortal Kombat, oh so much; starts off as the Outworld tournament champion, signs a peace treaty with the Shokan's mortal enemies the Centaurs (and making peace with Kung Lao) in Mortal Kombat 4 and sided with Edenia against Shao Kahn in Mortal Kombat: Deadly Alliance, before getting mortally wounded and saved by Kahn, siding with him afterward. If that wasn't bad enough, most of his endings have him gaining enough power to overthrow Shao Kahn, kill off the Centaurs, and ensure the Shokan become their own neutral group.
Kabal starts off as a member of the evil Black Dragons, becomes good, then reverts to evil.
While her actions and motivations in game play this straight, it's revealed at the end of her side story in the Playstation 2 and Wii versions of Resident Evil 4 that she's working for a completely different organization that's above both the U.S. Government and Wesker.
Cole McGrath in inFAMOUS due to the fact he has to decide on acting good or evil in outcomes.
EarthBound: Porky uses this one every time you meet him; he'll claim he's willing to repent of his misdeeds until he gets an opening to make a getaway, and then he's right back to plotting against Ness. In the original Japanese it's implied that (at least the first time) he really was willing to make amends, but he took Ness' silence to mean he wasn't willing to forgive.
Tales of Xillia has Alvin, whose loyalty jumps sides several times throughout the game, although being a sellsword (at face value, anyway) this is partially forgivable.
''Tales of Graces has Richard, who throughout much of the game is being possessed by the big bad
Marathon: Durandal the rampant AI in the first game. First he gives factual information to Leela, then sides with the Pfhor and kidnaps you, then gets bored and lets you return to Leela, then starts directly helping defeat the aliens invading the ship, then steals the Pfhor corvette for himself. In the second game, though, he's seemingly calmed down and stays your ally.
In Marathon Infinity, YOU learn the bad side of being a cybernetic soldier who takes orders and has no free will of his own: anyone considered an authority figure to you can command you to do their bidding, even if it means slaughtering your allies and if said leader is in full A God Am I mode.
Penelope starts off as a Heel in Sly 3: Honor Among Thieves while in contract by the Black Baron, who is really her in a costume. She becomes a Face upon joining the Cooper Gang following the Baron's defeat, but eventually betrays them to Le Paradox, and returns to being a Heel, in Sly Cooper: Thieves in Time.
In The Elder Scrolls III: Morrowind, Eydis Fire-Eye, Steward of the Balmora Fighters Guild hall, proves to be one if you intend to complete both the Thieves Guild and Fighters Guild quest lines. The Fighters Guild and Thieves Guild have a clandestine war going on, as the Fighters Guild faction leader and a few of his top lieutenants, including Eydis, are in the pocket of the Camonna Tong, Morrowind's native Mafia. One Thieves Guild quest has you bribing Eydis with a certain artifact to get her to switch sides. However, if you then complete the Fighters Guild quest line, she'll view you as a threat once you reach a high enough rank and attack, forcing you to kill her.