Zuko from Avatar: The Last Airbender does a beautiful Face–Heel Turn in the season 2 finale. Actually, he does a Face–Heel Turn, then a Heel–Face Turn, then another Face–Heel Turn, then a few somersaults, ending with another Heel–Face Turn. Say that three times fast. His first Face–Heel Turn came when he was 12. An innocent, well-meaning boy gets half his face burned off by his loving father. After this, he hunts Aang ruthlessly for his "honor." His second, and most exemplary Face–Heel Turn, came at the second season finale. After starting fresh in Ba Sing Se, Zuko has to choose between his honor and his Uncle. After a blatant "I Hate You" speech, he attacks Aang and returns home a hero, at least until his final Heel–Face Turn.
Book 4 gives us two more Face-Heel Turns. Kuvira went from Suyin's protegée to a power-hungry dictator who claims to want to bring peace back to the Earth Kingdom but really seeks control, Baatar Jr. who followed Kuvira and took a massive level in Jerkass in the process. Zhu Li also seems to perform a Face-Heel Turn in "Enemy At The Gates", pledging loyalty to Kuvira after finally getting fed up with Varrick for his poor treatment of her, but "Operation Beifong" reveals her to actually be a Fake Defector, who deliberately got close to Kuvira so she could sabotage her superweapon.
Harvey Dent going from the respected attorney he was to the dangerous criminal Two Face in Batman: The Animated Series is done as a serious Tear Jerker. He had already been an established and likable character beforehand who suffered from anger issues until a disfiguring injury pushed him over the edge and made his psychotic alternate personality become dominant, and Batman has never once stopped regretting being unable to save him or given up on swaying him back to being a good guy.
Albedo from the Ben 10 franchise did this. In a flashback from when Ben was 11, he was allied with Ben and Azmuth, and was at least a respectful, decent guy at the time. From Ben 10: Alien Force onward however, he is a major enemy of Ben Tennyson, for he did turn evil during the Time Skip between shows.
"Turf Wars", the last episode of the 2006 revival of Biker Mice from Mars, revealed that Harley, Vinnie's girlfriend and one of the Martian freedom fighters who rebelled against the Plutarkian invasion from the original 1993 series, became disfigured while trying to flee from the Plutarkians and sided with the Rats because she believed the Biker Mice abandoned her. The Biker Mice did not abandon her, and were in fact aghast to see an old ally become their enemy.
A Flashback episode of GoBots revealed that Cy-Kill was once Leader-1's best friend, but frustration over the leadership of Gobotron caused Xy-Kill to join the rebellion (and eventually lead it). In fact, the name of the episode where this is told is "Et Tu, Cy-Kill?"
Codename: Kids Next Door had an agent, Numbuh 274, who had appeared in a couple Season 1 and Season 2 episodes become a villain from Season 3 onward after turning 13. However, it turned out that he'd been working for the good side all along in the penultimate episode of the show.
The fourth-grade class president also began as a heroic character but, after the KND works to ensure his safe election, it's revealed that he's actually their enemy. The exact nature of his Face–Heel Turn is something of a mystery: while his blank eyes, Creepy Monotone and Father's Evil Laughter during his Face–Heel Turn implies that he'd been brainwashed, later episodes establish him as not only a perfectly willing heel, but one whose agenda has little connection to Father.
Denahi in Brother Bear, after he thinks a bear killed his brother Kenai (in reality, his brother Kenai was turnedinto a bear). He spends most of the film on a Roaring Rampage of Revenge trying to kill Bear!Kenai until the very end where Kenai is transformed back right before his eyes.
Parodied in Ed, Edd 'n' Eddy when, after a misunderstanding caused the other kids to beat up Captain Melonhead (Jonny) and Splinter the Wonder Wood (Plank), they became The Gourd and Timber the Dark Shard to get revenge on the cul-de-sac. Too bad the movie was over.
A fictional pro wrestling example. In one episode of Futurama, Bender becomes a popular robot wrestler named Bender the Offender. After his popularity fades, management turns him into the Gender Bender.
Demona in Gargoyles, who became obsessed with committing genocide against humans after her clan was massacred.
Green Lantern: The Animated Series: This happens to Aya after she shuts down her emotions and takes over the Anti-Monitor's body, becoming a Knight Templar bent on eliminating all organic life to the pointat she goes back in time to rewrite the creation of the universe. She comes to her senses when she accidentally nearly kills Razer.
In Iron Man: Armored Adventures, Gene Khan does this in spectacular fashion during the second half of the season finale. Given that the writers had spent the entire first season making this character friends with the hero, humanizing him and integrating him into the True Companions, this is actually fairly stunning, especially given that this show loves sympathetic villains being redeemed the way it does.
One could argue that Gene made his original turn at the start of the series, when he threw down his stepfather and took the role of Mandarin for himself. Outing himself to his friends after they out themselves as Team Iron Man just sealed the deal.
Whitney Stane has often straddled the line between good and evil ever since she's donned the identity of "Madame Masque", going from Unlucky Childhood Friend towards Tony to Stalker with a Crush to him, with murderous tendencies towards her father, to redemption, to a brief Anti-Hero stint as Madame Masque, and Laser-Guided Amnesia that led her to be Demoted to Extra. Her heel turn is permanently established in "Iron Monger Lives!", where she remembers Tony's identity as Iron Man and her time as Madame Masque. She returns as Masque to hatch an elaborate scheme in order to ruin Tony's life and kill his friends and family. By the time the episode ends, she seems to be continuing her villainous persona and her vendetta.
In Kim Possible, Shego used to be a superhero before becoming a villain. Various other characters have short heel turns, often for a single episode, including Ron at least twice.
Barnacle Boy in Spongebob Squarepants, however it's only for one episode over the fact he wasn't allowed to have an adult-sized Krabby Patty.
Star Wars: The Clone Wars: Senate Commando Captain Argyus (in Season 1), Clone Sergeant Slick (in Season 1 as well), Pong Krell (in Season 4), Barriss Offee (Started out as a heroine in Season 2, becomes a baddie in Season 5).
The Silver Surver on The Super Hero Squad Show was so corrupted by the Infinity Sword, that he turns his back on Galactus and even tricks Thanos into giving him the complete Infinity Gauntlet. It's rare for a Face Heel Turn to pull a Starscream, but Silver Surfer pulls it off well and becomes the new Big Bad till the end of the series.
In the second TMNT series, the real Oroku Saki was originally one of a group of warriors that defeated a powerful demon. However Saki absorbed the power and became the Tengu Shredder.
Vernon Fenwick in the first TMNT series, to a lesser degree. He is originally, for the most part, is an ally to the Turtles, however, at the beginning of the eight season (the first of the infamous Red Sky Era), after the Channel 6 building is destroyed by Shredder, Vernon then sides with Burne Thompson in seeing the Turtles as menaces to society, as they weren't able to save the building in time (and Shredder blew it up because he believed they captured Krang).
Gibbs from [adult swim]'s Titan Maximum. His Face-Heel Turn in the first episode generates the conflict for the rest of the series. Unfortunately, it seems that he's perhaps the only character with any shred of competence.
Lightning near the end of Total Drama Revenge of the Island after accidentally giving Cameron the win in "Eat Puke and Be Wary", upon which he not only Took A Level In Jerk Ass, but also he replaces Scott as the Big Bad.
Dave in the Pahkitew Island finale, after finding out that Sky is already in a relationship, upon which his Sanity Slippage gets even worse.
Dinobot in the Transformers: Beast Wars episode "Maximal No More." He does a Heel–Face Turn back at the end, though, upon realizing that just because everything's going according to Megatron's plans doesn't mean that Megatron isn't a dangerous madman.
Blackarachnia in Transformers Animated pulls her Face–Heel Turn during the (mainly) flashback episode "Along Came A Spider". We discover that when they were in the Autobot Academy, Elita-1, Sentinel, and Optimus went to an organic planet, even though it was forbidden, and they encountered giant spiders. Escaping from the spiders, Elita used her download power to borrow Optimus's grapplers, but ran out of time, falling into a pit full of the spiders when Optimus failed to catch her with his other grappler. She attempted to use her download power on the spiders, but, the spiders being organic, it turned her into a mutated part-organic, part-mechanical Transformer with one of the spiders as her alt-mode. The new signal type made her impossible for Optimus to pick up on his radar, and led him and Sentinel to believe Elita was dead, and Blackarachnia to believe they abandoned her, and she joined the Decepticons.
Why hasn't anyone mentioned Wheeljack from Transformers Armada? He has one after believing that Hot Shot abandoned him and turns Decepticon.
Back to Beast Wars, there is also Rhinox/Tankor in the sequel show Beast Machines.
Riven in season 1; he grows frustrated with the Winx and his fellow Specialists, and eventually abandons his group, starts dating Darcy, and feeds the Trix information about Bloom. In the 4Kids Dub, he's brainwashed. He went evil again in The Secret of the Lost Kingdom, but that was due to Mind Control.
Bloom twice in season 2 serves Lord Darkar, but that was because of Mind Control.
Aisha in season four. She join in the Nebula's group to kill the Wizard of the Black Circle and avenge Nabu's death. It didn't last long, though it was still pretty shocking.
Raimundo in the season one finale of Xiaolin Showdown. Shortly into season two, he reverses it and returns to his friends, but not without suffering some consequences and trust issues.
Omi undergoes an involuntary turn after coming back from the yin/yang dimension, leaving his good side behind.
Aqualad/Kaldur'ahm in season two of Young Justice, after he becomes embittered at his former friends for letting Tula die during a mission gone wrong and his own mentor, Aquaman, for hiding the truth about his real, supervillain father, Black Manta. Kaldur ends up joining him.
Turns out he only faked his turn and is deep undercover for the Team.
Quacky the Duck on T.U.F.F. Puppy. He used to be a happy, funny TV show host until his show got cancelled by the network president, forcing him to turn evil and get revenge by destroying all television.