Agents of S.H.I.E.L.D.: After being firmly on the bad guy's side in season 1, Grant Ward spends most of season 2 bouncing back and forth between helping Coulson's team and hindering them. However, the season finale seems to have cemented him as a villain.
Alias: Arvin Sloane for four-and-a-half seasons of the show.
American Gothic: Selena Coombs certainly seems to be riding one of these, or perhaps a seesaw. Aside from the moments when we see the weakening of her evil resolve and the good heart shining through (particularly the episode "Potato Boy"), the last several episodes of the series involve her repeatedly switching sides. It's hard to tell exactly who she's lying to at any given moment—Buck, Dr. Peele, or Caleb.
Lampshaded, where the character of Lindsay switched sides often enough that Angel decided to take pre-emptive action. Near the end of the series finale, Lorne, on Angel's orders, shoots him before he goes through the Face–Heel Turn phase again.
Angel himself, the no-good Irish lad turned into a bloodsucking demon turned into a mourning atoner still in the demon's body. And that was before the series began properly. During the course of both Buffy and Angel, He went on to lose and regain his soul several more times, revolving between heel and face each time. At one point, during a complex sting operation, he pretended to have turned evil again and then had to pretend pretending to be charming Buffy's mother. That's five stacked layers simultaneously!
Also Darla (though that one tended to have more logical reasons - whether she was a vampire or not, had a soul or not...)
Connor had more switches than anyone else in the series. He showed up in Season 3 as a Well-Intentioned Extremist taught by Holtz (also an example of the Well-Intentioned Extremist trope) to hate his father, Angel. He went from Heel to Face and back to Heel in Season 3, then switched sides (always thinking he was on the side of good) too many times to count in Season 4. In Season 5, given a normal life, he settled on Face.
Harmony. One of the best examples of Heel–Face Revolving Door, because she remained clearly the same person throughout and her switching sides fit into her conformist character. At the end, Angel tells her that he knew all along that she'd go back to Heel, because she has no soul.
Faith went from thinking being a Slayer was awesome, to discovering she really enjoyed killing and hurting people, to wanting Buffy to kill her in order to bring Buffy down to her level, to being freaked over Buffy almost killing her and wanting revenge for killing her father figure, to a Heel Realization, undergoes a full Heel–Face Turn in the last part of Buffy Season 7, to The Resenter in the comics, to a kinda sorta reformed Slayer, after attempting to kill Buffy again. At last count she's playing watchdog for Angel.
Throughout the series, Spike would switch between attacking the Scoobies and reluctantly joining forces with them for his own needs, even after becoming a somewhat ally in season 4. Heck, even when he got his soul back the final season had him murdering people again, though it turns out the First Evil was controlling him against his will.
Babylon 5: Londo Mollari takes a few spins through the door as the series progresses. At times it seems more like sides are picking him than the other way around.
Boomer: First she's Cylon sleeper agent, then she doesn't want to be one, then she fails to overcome her programming and shoots Admiral Adama. Then she tries to make peace between Cylons and humans and, failing that, she tries to kill her counterpart's daughter and betrays her model number, causing a civil war. Then she has a change of heart and escapes with the Final Cylon when the others want surgically to remove her brain. Then, faced with execution for causing the Cylon civil war, she knocks out another Cylon to take her place in the brig while abducting Athena's baby to use as a hostage in her escape plan which ultimately cripples the battlestar. Then she starts having second thoughts after bonding with Hera. Make up your damn mind, woman! If you weren't so flaky maybe more people would like you. At least Athena killed her after she returned Hera before she had the chance to change her mind again. To be fair, though, her constant mind-changing isn't entirely unjustified. if you flew all the way to some middle of ass nowhere planet to bond with the humans, only to have them start suicide bombing you, and then, on top of that, the man you love has married and is having a baby with the girl who shot you, then, well, you'd probably be a little peeved too. It's also worth noting that at least one set of those Heel Face Turns was faked (Rescuing Ellen was entirely a front so that she could kidnap Hera.)
It's mentioned several times by other Cylon models that this is a characteristic of the Eights, in that they're easily swayed. Even Athena calls them on it. In fact Athena's fanatical devotion to the Colonial cause may be an attempt to compensate for this perceived weakness in herself. That and the fact that the slightest indication of treachery would get her thrown out an airlock.
Gaius Baltar was even worse. The plot kept jerking him around from The Atoner to Les Collaborateurs. Not entirely his fault, since he had a phantom cylon in his head for most of the series, but still, would it have killed him to show some backbone once in a while? Signaled by his recurrent Beard of Evil: clean-shaven, he was The Atoner, sometimes even The Woobie. With stubble, he was a Dirty Coward, and usually a Smug Snake as well. On rare occasions when he actually groomed his beard, watch out.
And the tradition is carried on by Joseph Adama in Caprica. One week he's Daniel Greystone's best friend, the next he's sending his brother to kill Daniel's wife. One week he's recovering from Tamara's death, the next he's diving into a VR game to desperately try and find her. One week he's a stable, loving father, the next he's shooting up virtual drugs.
Jill is discovered to be a Fulcrum agent but says she was forced to, Chuck then sees that she was going to kill Sarah and arrests her in another episode, but then Chuck finds out that Jill was telling the truth and lets her go.
An even better example now is Chuck's mother in season 4. We had 5 episodes ambiguously building her up to be possibly good and working undercover, or possibly working for the bad guys. The sixth episode of the season has her appear and swear her innocence, seeking help to stop a dangerous weapon from getting out, only for her to betray everyone. Except, it turns out all of this, including shooting Chuck because she assumed he was wearing a bulletproof vest, was part of her plan in order to fool the bad guys. Casey then tracks down evidence that her entire cover story is a lie and she really did join the villain years ago. In the seventh episode, she once again claims she can prove her innocence and sends Chuck on an episode-long mission to find the proof. Except, this was all part of an even more brilliant gambit, as she was in fact tricking Chuck all along in order to bring herself and her boss to Orion's base and blow it up with Chuck and Sarah inside. ...AND THEN SHE SECRETLY HELPS THEM TO ESCAPE. That's at least six trips through the revolving door in two episodes, and nobody's entirely sure whose side she's on.
As it turns out the good guy's she's taking volkoff off from the inside
Dark Oracle: Omen suffered badly from this, due to a bad case of Chronic Backstabbing Disorder combined with a desire for Revenge and an unfortunate tendency towards partnering with those who were stronger and more evil than him. He's a villain at first, manipulating Cally as part of a plot for revenge on Doyle. He then tries to help Cally get rid of the comic book (partly out of a crush on her and partly out of a desire to hurt her Evil Twin, Violet) and gets trapped in comic world for his trouble. He returns, and helps Big Bad Wannabe Vern trap Lance in the comic world, pretends to help Cally get him out while secretly working for Lance's Evil Twin Blaze whom he actually frees, and then finally pulls a Heel–Face Turn and dies helping Cally free Lance and get rid of Blaze and Violet. Jeez man.
The Master does this quite frequently, partly because the fans love him and partly to demonstrate that he's just like the Doctor, only evil. Simm acts like this in The End of Time, but Ainley does it most dizzyingly in "The Five Doctors", going from "help the Doctor" to "help the bad guys" a handful of times in one story. Also the Ainley Master seems rather hurt that the various versions of the Doctor all suspect his motives.
Volume 3 Sylar, of all people. Just to show how crazy it's gotten: First, he was standard "killer" Sylar. Then he joined Angela Petrelli and tried to reform. Then he joined Arthur Petrelli against Angela Petrelli and tried to reform in a different way. Then he betrayed Arthur Petrelli and skipped town with another character. Then they go BACK to Arthur Petrelli. And then he becomes a serial killer again and goes AFTER Arthur Petrelli. After that, he gets split into a friendly "empty slate" body (which occasionally thinks it's Nathan) and unwanted dark passenger in Matt's head. When he finally manages to get body and mind back together, he is suddenly "impotent (sic)" at killing people and gets really nice and cosy towards Claire. Because, as we are learning, he wants to become socially accepted again. After being rejected by Claire, he is then trapped in his worst nightmare by Matt only to be saved and brought out by Peter Petrelli (he had a dream that Sylar would save Emma), after they were both trapped in his head for what seemed like years (but was actually only hours). Because of his near-endless torture experience from his nightmare, he turns good AGAIN and teams up with Peter.
HRG fits this trope as well. He is constantly shifting, so we are never entirely sure which side he is on save his own. We know his agenda is to protect his family, particularly Claire, which would put him on the good guys' side, but the methods he uses have alienated his family.
Nathan Petrelli also fits this trope, even better than HRG. In Volume 4 He went from Big Bad to good guy slightly less of a bastard guy.
Kamen Rider 555: Kiba Yuuji switches back and forth between helping and hating humankind several times during the story.
Lost: Due to the aggressively gray morality of the show, somebody either does a full 180, or is set up to look like they have, in almost every episode. The worst offender is probably Ben, with Sawyer running a close second, especially in the first few seasons.
Rumplestiltskin, whose unresolved personal issues and guilt over his chronic cowardice, trying repeatedly to redeem himself with Belle, who becomes his Morality Pet. After her memory is wiped, his focus returns solely to finding his son. After finding out that Henry is his grandson, making a good majority of the main cast his family as well, his motives and intentions become increasingly more ambiguous. In the first half of season 3, he travels with Emma, Snow, Charming, Regina, and Hook to rescue Henry from His father, Peter Pan, and later takes him down, killing himself in the process. In the second half, he is brought back by Neal and is controlled with the dagger by Zelena, who uses him to do her bidding, before marrying belle in the season finale. In season 4, he puts on an act of being changed, while really conspiring to cleave himself from the dagger, which would cost several lives to do so. After his plan is discovered, Belle uses the dagger to force him to leave town, but he later returns, and works with the queens of darkness to turn Emma, the savior, dark while trying to find the author of the book to write a new story in which villains get a happy ending. It turns out this was all to prevent the darkness from taking him over completely. The Apprentice removes it, but it leaves him in a coma, and the darkness breaks free, trying to take over Regina, before Emma uses the dagger to force it to take herself as the new host, becoming the new dark one.
In Season 5, Gold spends the majority of the first half of the season trying to be a better man after becoming mortal and powerless, again, before secretly enchanting Excalibur to transfer the darkness to back to himself upon Hook's death, becoming not just the Dark One (again), but the most powerful Dark One to have ever lived.
Regina enters the revolving door in Season 2, desperately trying anything to win back her surrogate son. Howewer, as of the Season 4 finale, she is undeniably a hero now.
Emma in season 5. After becoming the Dark One, she repeatedly bounces back and forth, making it a mystery even to the storybrooke residents if she's good or bad, and what her end game is.
Jenna. Initially she's against the Liars due to them being part of the prank pulled by Alison that led to her blindness, but later has a change of heart after Hanna saves her life. She assures the Liars that they can trust her, only for her to keep yet another secret from them: she regained her eyesight. There's also the fact that she's still a suspect for being A (albeit a less suspicious one as of recent episodes).
As of season 4, we have Mona: The reveal that she's the Big Bad of seasons 1 and 2 at the end of the latter puts her on the Heel side, then she's sent to Radley where she "reforms" and is integrated back into society in the second half of season 3. She tries to convince everyone that she's made a Heel–Face Turn now, and yet no one trusts her, still believing her to be evil. They were right, she was working for the second A. However, after almost being burnt to death in the season 3 finale, she tells the Liars that they're "all in this together", and joins them to try and unmask A. We have yet to see how much this will last though...
Prison Break: John Abruzzi. Also Mahone whose loyalties remain murky up until the end of the series.
Revolution: Nate Walker or Jason Neville. He saved Charlie's life in the episode Pilot. In "Chained Heat", Charlie manages to get the drop on him. In "The Plague Dogs", Nate helps to save Charlie's life from Ray Kinsey. In "Soul Train", Nate gets captured by Team Matheson and refuses to talk. He escaped and told Tom Neville what he knew, but he also helped Charlie to escape from Neville. In "Sex and Drugs", he reported to Monroe that Aaron had one of the pendants in his possession, but he left out a number of details in his report. In "The Stand", he decides not to help Tom Neville in bringing an air strike on the rebels, gets thrown out and warns Charlie about the air strike. The "The Song Remains the Same" has Nate officially join up with the rebels. Unfortunately, his past allegiances come back to haunt him in the episode "Clue" and nearly gets him killed when they think he's still working for Monroe. In the first season finale "The Dark Tower", Jason Neville seems to join up with his father when Tom Neville successfully takes over the Monroe Republic. However, there are already signs that things will break down between them sooner rather than later.
Lionel Luthor starts off moderately evil, becomes/is retconned to be completely evil, goes to prison, temporarily switches bodies with Clark and thereby absorbs some of his strong moral fibre (making him into a good guy), is convinced to readopt his villainous ways by an Evil Twin of Lex Luthor, and then spends several seasons stumbling drunkenly along the line between good and evil out of lust for Martha, before temporary possession by Jor-El converts him to the side of good until Lex throws him off of a building and he dies.
The two main villains of the series- Gul Dukat and Kai Winn both started out as smug, power-hungry backstabbers, and then went through a series of character arcs which gradually made them more sympathetic until they were Anti-Villains and almost good guys in their own right, and then both immediately turned 180 and became even more evil and vile than before, ending up as devil-worshipping cultists. Winn eventually experienced Redemption Equals Death, but Dukat became The Antichrist. One of the writers said that, expecially in Dukat's case, this was intended to make them better villains, showing that they had the capacity to be good, decent people- they just consciously chose not to be.
Star Trek: Voyager: In-universe example. In the episode with the holonovel about the Maquis mutiny, Tom Paris switches sides whenever it's convenient. Holo-Chakotay wises up fast and sends him off to a position where he doesn't matter to the story.
Although Castiel is unarguably trying to be the good guy, he appears to have been trapped in this revolving door since his first appearance. He starts out as the angel that rescued Dean from Hell, but then it's revealed the angels have plans for Dean and expect him to do exactly as they say even when their plans are morally ambiguous to say the least. Castiel starts to have doubts and sympathize with Dean, eventually twisting the rules to help Dean. But then he gets dragged off to Heaven and forced back into line, betraying Anna and setting Sam free to go start the Apocalypse, before he betrays Heaven for good and sides with Dean a couple of episodes later. He spends most of the fifth season on the Face side of things, with the exception of his Temporarily a Villain role in "I Believe The Children Are Our Future", but appears to have jumped back into the revolving door as of season 6. He makes a deal with Crowley, but he does so in order to fight Raphael and prevent the apocalypse from re-starting. In order to carry out his plan though, he is forced to lie to and manipulate the Winchesters while carrying out some pretty morally ambiguous schemes. He undoes some of the worst ones though rather than risk the Winchesters, but ultimately finishes the season on a Heel note, having absorbed millions of souls from Purgatory and declared himself the new God. He seemed to come back to himself within an episode or so of the seventh season and asked for forgiveness only to be taken over by Leviathans who then, a few episodes later, appeared to liquefy him. About halfway through the season, he turned up again with amnesia. He got his memory back and took the broken wall in Sam's mind onto himself, effectively bringing Sam back to normal, but landing himself with an incredibly messed up head. As of the end of Season 7, he seems to be on the Face side, having made a Heroic Sacrifice. As of the middle of Season 8, he's apparently back to Heel, being Brainwashed and Crazy for Naomi. In the episode "Goodbye, Stranger", he leaves both sides behind and goes off on his own. Expect this section to expand continually.
Crowley is Castiel's opposite; he desperately wants to be the Big Bad, but circumstances and greater threats keep forcing him into Enemy Mines with the heroes. When we first meet him in season 5, he helps the heroes fight Lucifer because he correctly believes that once humanity is destroyed, Lucifer will turn on the demons. Once Lucifer is dealt with, however, he declares himself the King of Hell and spends most of season 6 as an antagonist. But once season 7 rolls around the new threats of Castiel and the Leviathans force him to reluctantly aid the heroes again for a return to the status quo. But of course, as soon as that's dealt with, he immediately betrays them and goes back to being a bad guy for season 8. Season 8 ends with Crowley's humanity being partially restored and Knight of Hell Abbadon announcing her plans to usurp Crowley's throne, so it wouldn't be surprising to see him back on the side of good (or at least as close to the side of good as he ever gets) for season 9.
In Season 9, Gadreel's allegiance is all over the place. He starts out as a guardian in Heaven, then he lets Lucifer inside the Garden of Eden and is punished for his crime. After his unexpected release he tries to atone by helping Dean save Sam, only to be convinced by the conniving Metatron to join his new army. He joins the Winchesters again, but the vengeful Dean is having none of it. Gadreel eventually helps Castiel infiltrate Heaven but fails and commits suicide in a final act of atonement.
Teen Wolf: Viewers can look forward to seeing whether Derek is going to be a good guy or a bad guy in any given episode. He is never genuinely evil though.
His uncle, Peter, might qualify better. He's killed several of the Big Bads, and has extensive knowledge of the supernatural that he will use to help the heroes, but only if it's to his benefit. The other characters are mostly aware of this, and never fully trust him.
Damon pretty much lives inside the revolving door. Of late he has been ostensibly a good guy, at least in terms of larger motivations, but he still always seems to find time to relapse and kill people to keep things interesting.
Also Isobel. Really, you never know whose side that girl is on.
Wizards of Waverly Place: Max did this is one episode, taking Justin's side, then Alex's side, then back, depending on who looked most likely to win the weekly conflict at that exact moment. He also announced to both siblings when we was doing this.