The first episode of Archer was tentatively entitled "Mole Hunt", where Archer starts a rumor about there being a mole in ISIS, causing everyone to, well, hunt for the mole. And it turned out there really was a mole.
It is revealed in "Mud Is Thicker Than Water" that a Tetramand named Gorvan has infiltrated the Plumbers and has been stealing their weapons for Psyphon and his minions. Of course, the Plumbers were smart enough to have Lucy infiltrate Psyphon's gang as another mole.
Gorvan also did this in the video game Ben 10 Alien Force where he is a rogue Plumber who has been stealing alien tech to help the Highbreed build their Weather Tower in preparation for the war. He even tricked Ben Gwen and Kevin into stealing some of the items for him.
Chip Whistler in Big City Greens becomes this in "Reckoning Ball". After discovering the Greens' kindness and heeding advice from Bill to "put in the work" before he can "reap the rewards", he pretends to apologize for his misdeeds and make amends with them, which is enough to woo Cricket into believing he really means it, and is the first to sign his forgiveness contract as proof before the rest sign as a family, but Gramma Alice remains suspicious. Now the CEO of Wholesome Foods and with his dad out of the picture, this gambit eventually results in the shutdown of Big Coffee and an ultimate battle to protect the Greens' legacy before it is destroyed forever by Chip's megastore expansion. Cricket soon realizes what he did and ultimately regrets his actions.
Butt-Ugly Martians has Shaboom Shaboom, a female Martian on good terms with B-Bop A-Luna, 2T Fru-T, and Do-Wah Diddy who pretends to be on Emperor Bog's side so that he remains unaware that the Butt-Uglies have abandoned their mission to invade Earth out of coming to love the planet.
Codename: Kids Next Door has one in the form of Chad Dickson (a.k.a. Numbuh 274.) Starting in the Season 2 finale when Chad has his Face–Heel Turn moment by trying to hurl the KND Moon Base into the sun and thus becoming a villain for the rest of the series until the second-to-last episode which reveals that he was a double agent the whole time and that all off his attempts were actually him preventing other villains from doing the same to the KND and being successful.
Danny Phantom: Danny suspects new love interest Gregor is The Mole for the Guys in White because of his white clothes and his coincidental arrival at the same time as those guys. He's not. Unfortunately, the reveal was too easy to point out. Though I didn't suspect he was a Fauxreigner!
In Justice League, it turns out that Hawkgirl has been The Mole the entire time. Albeit one who did a Heel–Face Turn and left feeling she required self-imposed penance, but still one that they had a hard time trusting for the rest of the run of the series.
An odd variation of the theme occured in the Batman Beyond multi-part episode "The Call". After a member of the Justice League was injured in a suspicious accident, Superman recruited Terry in an effort to find out if there was, indeed, a traitor among their members. As it turned out, Superman himself was the traitor, but not intentionally; he was under the Mind Control of one of the aliens he had kept at the Fortress of Solitude for so many years.
In Season Two of Dragons: Race to the Edge, the gang's ally Heather becomes one when she manages to infiltrate the Dragon Hunters, passing information to the Riders to sabotage their hunts, until she is finally exposed and forced to join the Riders full-time.
"The Menace from Space". Dr. Kasdan, an expert on interstellar biology, is added to the team when it investigates a manned space flight which has been infiltrated by a dangerous space life form. He turns out to be a traitor working for a hostile government and tries to sabotage the mission so that the ship will crash in the U.S. and release the life form there.
"The Mind of the Master". When Guru suffers brain damage as the result of an attack by an unidentified opponent, the team must miniaturize and enter his brain to repair it. They take along a man who is Guru's oldest associate, and who is revealed to have been the man who attacked him.
G.I. Joe: Renegades has a couple of benevolent examples. Lady Jaye subverts Flint's efforts to catch the Joes, and Breaker had an inside man in Cobra for awhile.
An episode of Harvey Birdman, Attorney at Law had a trial for Morroco Mole, accused of being a terrorist, but Birdgirl reveals he was this trope instead. The charges were dropped and Morocco was ordered to stay away from Judge Mentok's yard.
"The Quetong Missile Mystery". Lieutenant Singh of the Quetong Police has sold out to General Fong.
"Skull and Double Crossbones". Jose the cook is secretly a member of the pirate crew stalking the Quest team.
"Treasure of the Temple". The Indian guide Montoya is in league with a ruthless treasure hunter.
"The Curse of Anubis". Dr. Ahmed Kareem is actually the villain.
So the Drama, the (first) Grand Finale to Kim Possible, has a rather obvious mole, who nonetheless fools everyone.
My Little Pony: Friendship Is Magic: Fluttershy becomes one in part 1 of "The Cutie Map" so she can eavesdrop on Starlight Glimmer and find out where she keeps the Mane Six's cutie marks.
Nascar Racers: Lyle was this at the beginning as he was officially a Fastex driver but was spying on them for Garner Rexton.
The New Batman Adventures episode "You Scratch My Back" has Nightwing acting as this to fool Catwoman into Batman's plot of bringing her and the villain of this episode in.
The Powerpuff Girls capture Rowdyruff Boy Boomer (episode "Bubble Boy") then they have Bubbles infiltrate the other Rowdyruffs disguised as Boomer. It speaks volumes that Brick and Butch's intelligence didn't catch on as Boomer doesn't have a high pitched voice and baby blue eyes.
Scooby-Doo! Mystery Incorporated is full of moles and traitors, as you'd expect from a show that exemplifies the Gambit Pileup. Marcie (a.k.a. Hot Dog Water) reforms, joins Mystery Inc., betrays Mystery Inc. to Mister E, betrays Mister E for Mystery Inc., and finally dies to slow down Pericles' robots so the gang can escape. Freddy's real parents are obvious spies from the start, but who they're working for changes halfway through the plan, and they die while attempting to change allegiances again.
Plankton is this in "New Leaf", as he pretends to go out of business and turns the Chum Bucket into a gift shop to trick Mr. Krabs into handing the secret formula to him. Until it's revealed he was Out-Gambitted and Mr. Krabs knew all along.
SpongeBob becomes a brief one in "One Coarse Meal" after confronting Mr. Krabs for tormenting Plankton into suicide with his whale phobia and lets Plankton in on Mr. Krabs' fear of mimes to get back at him.
At one point, this is parodied when there's a squealer in the group.
Fat Tony: Now some unpleasant news. I have learned that someone in this room is a squealer. Legs: We've narrowed it down to either Johnny Tightlips or Frankie the Squealer. Frankie: Okay, it's me! I can't help it! I just like squealing! It makes me feel big!
In "A Star is Torn", Lisa enters a singing contest hosted by Krusty, with Homer as her manager. After she fires Homer for being a Stage Dad, he begins managing her competitor... who then loses all his fans and popularity in the final. Homer shows himself to be this to Lisa at the end.
Near the end of the Star Trek: The Animated Series episode "The Jihad", party member Charr reveals himself as the person behind the theft of the Soul of the Skorr.
"Cloak of Darkness": Captain Argyus, head of the Senate Commandos; the wow-factor in this case comes from the fact that, as an elite bodyguard in the employ of the Galactic Senate, most would expect him to be as loyal as they come.
Clone trooper Sergeant Slick sells out the planet Christophsis in "The Hidden Enemy". What made it more surprising than Captain Argyus is that he's a clone. Men who you would not think would do that. Or be capable of such a thing due to their training/programming.
The first season has Senator-in-Exile Gall Trayvis, who, working for the ISB, posed as a Voice of the Resistance to monitor rebel cells and lure troublesome ones such as the Ghost crew into "accidents". The crew winds up blowing his cover by escaping the trap set for them.
In "Breaking Ranks", Ezra, while undercover as an Imperial cadet, befriends a fellow cadet, ZareLeonis, who's joined the Imperial academy to search for his sister, an Imperial cadet who mysteriously vanished. He chooses to stay behind at the end of the episode, but agrees to give the Ghost crew intel.
In season 3, Agent Kallus has become disenchanted with the Galactic Empire, but instead of defecting to the Rebellion he becomes a spy who reports under the code name Fulcrum. Conveniently, as a high-ranking member of the Imperial Security Bureau, he is the one responsible for rooting out spies and traitors in this particular sector of the Empire, and thus in a good position to ensure that spies and traitors don't actually get found while framing other Imperial officers for his own actions (or would've been if not for Grand Admiral Thrawn arriving in the sector).
Steven Universe: Played for Laughs in "Hit the Diamond". Garnet unfuses so that Ruby can infiltrate a team of enemy Gems — and she's absolutely TERRIBLE at it, and only avoids being caught because the people she's trying to fool are complete idiots who can't even count themselves properly.
Terra, which is an adaptation of a famous story arc from the comic's 1980s heyday, "The Judas Contract". Unlike the comics, it's done with a sympathetic angle towards Terra.
Bumblebee is a mole for the Titans in Blood's school, although Cyborg doesn't know it and tries to fight her for real. When Brother Blood finds out about this, he is not amused, as this was the second mole found in his school in such a short period of time (the other being Cyborg).
Brother Blood:[getting more agitated as he continues speaking] Another spy? Tell me, was anyone at my school actually there to LEARN? Bumblebee:[gets into a fighting pose] I learned plenty.
Played with in the first season finale. Sladereveals his season-long Evil Plan to Robin: Slade had lured Robin away from the rest of the Titans, leaving them to deactivate his "Chronoton Detonator" which was actually a device that injected them with deadly nanites, allowing Slade to kill them with the push of a button. After this reveal, Slade made Robin his new apprentice, thus making Robin somewhat of a Fake Defector, albeit with the villain commandeering the operation specifically designed to make the unwilling defector comply and prevent him from informing his comrades because then, they would most assuredly die, thereby making the goodies, not the bad guys, the ones to be deceived by the hero's false defection. Following the establishment of his apprenticeship under Slade via a little crime spree and a show-down with his ex-teammates Robin's friends fully believe that he has been lost to The Dark Side, for good. This makes the discovery that Robin was really on their side the entire time all the more surprising, from their P.O.V.
As shown on the characters page, Owen from Total Drama Action was one for Chris, although he was rather reluctant, and had a legitimate reason for doing so.
Shockwave from Transformers: Animated. The Autobots know him as Longarm Prime, head of Autobot Intelligence.
Sideways in Transformers: Armada. After switching between the Autobots and Decepticons several times, he is revealed to be an agent of Unicron, making both sides fight each other to fuel him with their hatred.
And Sideways in Transformers: Cybertron, not to be confused with the Sideways mentioned above, is a mole in the Decepticons working to...actually, it's never quite clear why he's there.
He wants the Cyber Planet Keys for himself, so as to annihilate Gigantion and avenge his homeworld Planet X, which was destroyed by one of its own weapons in a war with Gigantion. He eventually settled for being with the Decepticons, because he felt their aggression would serve him better. He sided with Starscream eventually, betting on the madbot Determinator who had the bearings to attack all the Autobots at once to get what he was after. Eventually Sideways bailed on the 'Cons entirely after almost getting vaporized by Optimus Prime, and thereafter worked solely with his fellow survivor Soundwave.
A major plot point is that apparently a member of the team is a traitor. Artemis seems to the most obvious candidate, though her debut episode and an issue of the tie-in comic make it seem like this is a red herring. An episode had the team leader, two supervisors, a member, and an outside friend sit down and discuss the possibilities. According to them, Artemis has suspect connections, Conner has suspect origins, and M'gann has a suspect story, while Wally, Robin, and Kaldur are "above suspicion". In the end The mole was nobody on the team. Wally, Robin and Kaldur were above suspicion after all, while Artemis, Superboy and M'gann were all blackmailed, but opted to come clean about their secrets rather than betray the team. Red Arrow was the mole (and he was an unknowing brainwashed one), and he was to be the mole for the Justice League (having worked his way into their ranks by the end of the season) and not the Young Justice team. Implying they had a mole in their team was just to sow dissent.
In season 2, Kaldur has pretended to undergo a Face–Heel Turn to spy on the villains. He is later joined by Artemis, who has faked her death and assumed a new identity.
In season 3, Terra and Helga Jace, the former is set up to be rescued by Nightwing's team and reports to Deathstroke, while the latter joins them earlier on and reports to Ultra-Humanite. Only Terra's is played sympathetically, arguably even more than in Teen Titans above, as while she still went through with attacking her teammates in TT before undergoing her Heel–Face Turn, she undergoes hers in YJ before she even attempts successfully to hurt anyone.
