On Agents of S.H.I.E.L.D. (part of the Marvel Cinematic Universe), a mass face heel turn occurs in the second half of the first season: Turns out about half of S.H.I.E.L.D. is actually Hydra sleeper agents, a massive infiltration dating back decades. Thus, this is one of the cases where always-been-heels characters are outed as such. Notable examples include:
Grant Ward, a notable member of Coulson's team (and the main cast).
John Garrett, Coulson's friend and colleague and a command-level S.H.I.E.L.D. agent, who turns out to be a mid-ranking Hydra mastermind.
In related events happening at the same time in Captain America: The Winter Soldier, World Security Council Secretary Alexander Pierce, the ultimate boss above Nick Fury and all of S.H.I.E.L.D., turns out to be the mastermind of a Hydra plot to take over the world, and recurring S.H.I.E.L.D. agent Jasper Sitwell is revealed as a Hydra agent as well.
...and Anna Sheridan, who could be assumed to be a good person prior to getting Shadowed.
In a way, the entire Minbari race after the disastrous first contact with humanity. Mostly reverted later.
The third season of Degrassi revolves entirely around Manny and Sean turning heel, then slowly turning back to face.
Half the cast of Alias. Double-agency was a big part of the premise of the show, so it is to be expected.
Perhaps most notable was Lauren, Vaughn's (first) wife, which was probably supposed to be a big surprise, but which everyone saw coming anyway.
There were several in-show Face-Heel Turns that the audience was in on before the characters were:
Sydney was a double-agent for the real CIA, supposedly working for SD-6, and when she revealed herself to Dixon, he saw that as a face-heel turn. He came around eventually.
Francie was killed and doubled, and her doppelganger worked for a season as a bad guy, and when she was revealed, Sydney would have seen it as a face-heel turn (mitigated by the fact that she wasn't really who she looked like).
Sydney's mother did this over and over and over. It's not a spoiler because it's a defining trait of her character, and in the end you're never really sure which side she was on.
Vaughn appeared to do this at the end of season 4, but then it's pretty gray as to what's happening. The show has so much of this trope that the audience expected it (or at least was hardly surprised), and then the turn was subverted because he didn't really turn evil.
On Lost, Michael was of the Well-Intentioned Extremist variety, as he just wanted to save Walt, his son. He felt really bad about it, but there's varying opinion over whether or not we should feel sorry for him.
Charlie performs his when he kidnaps Aaron and Claire finds out he's a junkie. He had recently fought his demons, won, and turned around from a spoiled jerk to a almost hero. Then they demonize him again. May have involved the writers strike.
Locke also tagged along with the Others for a while, but he didn't really switch sides (though he certainly came close to being an out and out villain during a portion of Season 4, where his leadership was borderline tyrannical.)
Claire and Sayid in the final season, due to being infected by The Sickness. Both eventually fight their way out of it in the end.
Gul Dukat was one of the more interesting 'grey' characters (along with fellow Cardassian Garak). Most of Dukat's crimes were committed way before the series started, so the fans would not automatically hate him along with Kira Nerys. It was more of case the DS9ers were warming up to him, especially when he embarked on his one-bird-of-prey crusade against the Klingons. But as soon as he is sees the chance to 'make Cardassia strong again' (i.e. get himself into a position of power again) he does indeed remind everyone that sometimes Good Is Dumb.
Eddington is a more straightforward example from Deep Space 9.
Angel in Season 2 (starts with "Innocence"), Willow in Season 6 (starts in "Seeing Red") and Faith in Season 3 (starts in "Bad Girls" and continues with "Consequences"). All three get subsequent Heel Face Turns.
Angel's Face–Heel Turn happened due to having what is later described as a "moment of perfect happiness" which was his night with Buffy. This activated the Curse Escape Clause which brought back his original self, the incredibly evil Angelus.
Willow's is far more this trope than Angel as she was always the same person (albeit far, far more angry). She even says later that she remembers exactly how it felt and why she was doing it - and that it felt pretty good. Dark Willow is Normal Willow on the ultimate despairing rage power trip.
Giles in "The Lost Slayer" novel Bizarro World, in his vampire version.
On CSI NY Marty Pino, who went from recurring coroner to drug dealer processing body parts from victims for the drugs they contained.
Dr. Zack Addy, who turned out to be the serial killer's apprentice on Bones. He didn't actually kill anyone and it's more of a case of a weak will being overpowered by a strong one, but only Sweets knows that Zack prefers to be thought of as insane since he wouldn't survive prison. Regardless, his friends still love him (to the confusion of his replacements)
Sweet-natured Kes returns to Voyager to crumple bulkheads and anonymous ensigns in "Fury". It turns out she's angry at her former friends because...well it's never really explained. But don't worry as everything's back to normal by the end.
Kes was supposed to be upset over being talked into leaving all of her people and life behind to travel to the middle of nowhere with Voyager's crew, and the episode's plot was about her trying to go back in time and convince her younger self to bail while she still had the chance. Given her Ascended to a Higher Plane of Existence exit in "The Gift," it was likely a case of With Great Power Comes Great Insanity.
In the reimagined Battlestar Galactica, Felix Gaeta leads a failed mutiny against Admiral Adama, resulting in his and Zarek's deaths.
Earlier on in the series, Boomer appears to have joined Cavil's side in the Cylon civil war, later helps the final Cylon escape from exploratory brain surgery and gives her lover a literal Imagine/Hope Spot then steals her "twin's" daughter only to bond with her "niece" and give her back and is finally killed by her "sister".
In the final season of Burn Notice, Michael Westen goes deep undercover for the CIA to capture a criminal, James Kendrick. During his time undercover, Michael learns that James is a Well-Intentioned Extremist who made it his mission to go after the villains that the government wouldn't. Michael doesn't agree at first, but slowly becomes impressed with James' way of doing things. When the time comes to finally apprehend James, however, Michael learns that the leader of the extraction team is none other than Ax-Crazy murderer Simon Escher. After Michael kills Simon, he reveals the truth to James, betraying the CIA, the agency that burned him and put a psychopath like Simon in charge.
24 embodies this trope. Most seasons have at least one of The Mole at some point. Sometimes this turns out to be misleading, with a few Fake Defectors, but there are several infamous true face heel turns. Going back to the first season was Nina Myers, who turns into a recurring villain for two more seasons. Most recently was the even more drastic Tony Almeida, whose Heel–Face Revolving Door led the audience to be surprised by the (second) revelation that he was a villain, despite the fact that this was technically common knowledge months before the season even began.
A surprising one is that Jack Bauer himself undergoes something of one in the final season. After Renee Walker is killed and he gets screwed over by President Taylor when she effectively sells her soul to Charles Logan and undergoes her own FH Turn, he sets out on his own. Initially it seems like he's still trying to just do the right thing and expose the cover-up that Taylor's involved in, but when he murders Dana Walsh in cold blood even though she wasn't directly tied up with what happened to Renee it becomes clear that all he's after is vengeance regardless of the consequences. He gets so consumed he nearly starts World War III solely in the name of revenge, and it takes Chloe to literally talk him down at the eleventh hour. But by this point his actions have still effectively screwed him over and left him an international fugitive.
Doctor Who's own 10th Doctor went a little overboard (shall we say) in the episode "The Waters of Mars" when he finally realized he was the only Time Lord left in the Universe and didn't have to follow their rules anymore. He became megalomaniacal, the "Time Lord Victorious!" until the episode's heroine corrects his mistake. By killing herself.
Ashes to Ashes Season 3 kicks off with the introduction of new DCI Jim Keats. He seems like an upright, intelligent guy who even Gene Hunt begrudgingly respects - mainly because Keats is allowing Hunt to operate the way he wants to operate and isn't interfering the way other IAB officers would. He repeatedly tells Alex that he wants to help her, and he knows she has a larger purpose in this world. He makes overtures to the rest of the CID gang - Chris in particular - even bringing over a bottle of champagne to celebrate their closing a case. And then, about five minutes before the end of the episode, he walks into Gene's office, closes the door, and delivers one of the most scathing denouncements of Hunt and his people we've ever heard, and vows to bring Hunt down, no matter what.
Chuck: Daniel Shaw is an all-American hero, willing to die for his country, but when he finds out thanks to the Ring that Sarah killed his wife, he joins the Ring setting on killing Sarah for revenge; this turns out to be fatal, as Chuck kills him in order to protect Sarah.
Shaw does survive, though not without super-advanced medical help, and returns later on a grand plan to take over every major American intelligence agency while framing his former allies as traitors before executing them. If that wasn't enough, he gets his own Intersect and kills Chuck's dad.
In the Merlin (1998) series, Lord Lot and Morgan Le Fay both turn against Arthur and Merlin.
As of the finale of season 3 of the BBC's Merlin (2008), Morgana has finally completely turned against Arthur, Merlin and the rest of Camelot, and, with the possible death of Morgause, is in a prime position to take over as the Big Bad of the next season. Technically she was an enemy right from the beginning of season 3, it's just that now everyone knows about her Face Heel Turn instead of just Merlin and Gaius (and Gwen later on).
The "face-heel-turning" actually begins that the start of Series 3 after Morgana returns to Camelot after going missing for a year and becomes The Mole for Morgause and begins doing things like killing people in cold blood and threatening Merlin who unwittingly provokes her move to the dark side by attempting to kill her (for valid reasons) at the end of Series 2. The face-heel-turning of Morgana is amplified by the fact the first two seasons spend extensive time establishing the character as sympathetic and on a few occasions heroic.
In Series 5, Mordred goes from the Adorkable, loyal youngest knight to Arthur's killer after the girl he loves is executed for trying to kill Arthur.
In the miniseries Thumb Wrestling Federation (this sorta fits here), former Dextera member Evil Ira left for the Sinistras, simply because being good while he has evil in his name was too confusing.
In season 6 of Supernatural, the Big Bad of the season, to whom both Crowley and Eve played Disc One Final Boss, is revealed to be Castiel, who has decided that to defeat Rafael and put Heaven on the right track, anything is acceptable - in this case, taking on a million souls. The Winchester boys do their best to stop Castiel throughout the final episodes of the season, while he continues to plead for them to accept him and his reasons for evil.
Stefan Salvatore from The Vampire Diaries at the end of season two and for most of season three. Klaus reverted Stefan into his darker alter ego, the Ripper.
Duncan MacLeod does this for two episodes in Highlander: The Series, while he's possessed by the Dark Quickening. His good and evil sides finally battle after Methos drags him into a magical hot spring, and his goodness wins, enabling a Heel–Face Turn.
EastEnders - James Wilmott-Brown started out as the friendly face of the brewery, then bought his own bar, got obsessed with barmaid Kathy, and eventually raped her.
Gets surprisingly flipped halfway through the fifth season when Walt, having reached the top of his empire, having taken his operation global realizes that he has made more money than he could ever hope to spend and far more than he even set out for initially. This leads him to decide he is out of the game, make amends with his former business partner by giving him the money he's owed and try to start over fresh with his family. And then his DEA agent brother-in-law finally figures out he's drug dealer.
Forms the basis of the main plot of Homeland, with a CIA agent convinced that a formerly imprisoned U.S. Marine has been turned into a terrorist during the years of torture he'd endured.
Debbie Pelt performs a Heel–Face Turn offscreen after season 3 and then this trope (onscreen) in season 4.
Bill Compton started working for the Vampire Authority and went from mainstreamer to full-on Vampire Bible fanatic, slaughtering humans everywhere and doing all in his power to make vampires the dominant force on the planet.
Ollie Reeder in The Thickof It. He starts off as a somewhat unconfident and idealistic geek, gradually becomes a bit of a jerk and eventually transforms into an amoral and treacherous manipulator who is willing to throw anyone under the bus to improve his own career.
Slade Wilson starts out as a hero in Arrow, but after he learns of Ivo pulling a Sadistic Choice on Oliver that results in Shado's death, combined with the Mirakuru's effect on his mind, he turns on Oliver, blaming him for what happened more than he does Ivo.
Pretty Little Liars: Spencer Hastings, who joins the "A-Team" after Mona convinces her to, claiming she has information about Toby. It is revealed that he is not actually dead and she has a Heel–Face Turn and begins using her newfound alliance to stay ahead in the game.
Shane in The Walking Dead does this during the course of the first two seasons. Subtly at first, but rapidly gaining speed. Until his death.
House of Anubis: Jason Winkler joins the Secret Society early on in Season 1, betraying Patricia in the process. It's a bit of a complicated case as Jason still did care about the students (Patricia especially) and was only in on it to save himself from dying of a degenerative illness. He never did anything bad beyond being on Victor's team, and even tried to save the students from Rufus in the finale.
This also applies to the Sinners, who, after getting their souls stolen practically become sociopaths with no allegiance to anyone but Ammut and Robert Frobisher-Smythe. They were all brought back to normal later.
Heroes Reborn: In the years that have passed since Heroes originally aired, it's revealed that Matt Parkman has converted to the side of evil, working for Erica Kravid and Renautas Corporation as the Director of Sunstone Manor, a secluded property where specials are held prisoner and brainwashed by Matt into staying.
Game of Thrones: Olly is Jon Snow's trusted steward until he helps Alliser Thorne murder Jon as revenge for the latter saving and forming an alliance with the Wildlings.