Terra in Teen Titans, 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 an sympathetic angle towards Terra.
Also in Teen Titans, 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.
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 Face–Heel Turn to spy on the villains. He is later joined by Artemis, who has faked her death and assumed a new identity.
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.
Star Wars: The Clone Wars has featured two such characters. The first was R3-S6, a pseudo-Suspiciously Similar Substitute for R2-D2 who briefly replaced the famous droid after he was captured, and tried to mask his attempts to kill Anakin and co. as accidents. The second and more surprising of the two was Captain Argyus, head of the Senate Commandos; the wow-factor in this case came 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.
There was another example, Clone Trooper Slick sold out the planet Christophsis in the episode "The Hidden Enemy". What make it more surprising than Captain Argyus is that it was a clone. Men who you would not think would do that. Or be capable of such a thing due to their training/programming.
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.
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!
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.
Marcie (a.k.a. Hot Dog Water) in season 2 of Scooby-Doo! Mystery Incorporated. After Daphne departed with a new boyfriend, Velma took HDW in as a substitute. But after Daphne returned to the gang, HDW was given her walking papers. HDW is in cahoots with Mister E in finding the lost treasure of Crystal Cove, and she's playing Velma like a violin.
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.
Nascar Racers: Lyle was this at the beginning as he was officially a Fastex driver but was spying on them for Garner Rexton.
"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.