In Metalocalypse, when Toki gets fed up with always being the child friendly one and then starts burning the lair with a flamethrower.
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.
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.
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.
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.
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.
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.
Gibbs from [adult swim]'s Titan Maximum. His heel face 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.
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.
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.
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.
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.
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.
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.
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 point that she goes back in time to rewrite the creation of the universe. She comes to her senses when she accidentally nearly kills Razer.
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.