Ben 10: Omniverse: 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 a Reverse 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.
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 HeelFace 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.
"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.
Nascar Racers: Lyle was this at the beginning as he was officially a Fastex driver but was spying on them for Garner Rexton.
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.
"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.
Star Wars Rebels: 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.
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.
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.
In season 2 of Winx Club, the new teacher Avalon is actually Darkar's spy in Alfea. The real Avalon is locked up in Darkar's dungeon.
A major plot point in Young Justice 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.
A recent 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". Make of that what you will.
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 FaceHeel 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 HeelFace Turn, she undergoes hers in YJ before she even attempts successfully to hurt anyone.