The comic series Fables has had several—Rodney Greenfield (who pretends to be a Mundy, not a Fable, and who the reader knows is a spy from the end of his first appearance), the ironically named Trusty John (he IS trusty—just to his original master, who has joined the Adversary), Red Riding Hood (actually two different shapeshifting witches—the second being Baba Yaga), Ichabod Crane, and Bluebeard—although the one that he is secretly helping is Goldilocks, not the Adversary.
Mondo from Generation X was revealed to be a traitor planted on the team to help destroy it from the inside. He reveals his teammates' weaknesses to his master, longtime X-Men foe Black Tom Cassidy.
Iron Man's weakness for the ladies has led more than one of his enemies to employ a Femme Fatale Mole. In particular, Obadiah Stane used Indries Moomji this way with devastating effect. (She was the "Queen" among his chess-themed agents.)
Part of the premise of DC's 1988 Crisis CrossoverMillennium was that at least one character in every book was revealed to be secretly an agent of an evil alien robot cult. Since this was imposed from above on the hapless writers, the results were...variable.
20 years later, Marvel pulled off nearly the same thing in Secret Invasion, rather more successfully. For one, there was much better coordination between writers and the editorial staff; for another, they didn't automatically mandate "one character per book", which kept the readers guessing.
Runaways had a particularly shocking Mole in its first arc.
Sonic the Hedgehog: A recent retcon and a bit of Arc Welding have made it so that Geoffrey St. John's recent apparent Face-Heel Turn is actually this, stating that he's actually been working for Ixis Naugus since before either of them were even introduced.
Several are used in the Squadron Supreme limited series as part of a plot to stop the heroes' efforts to turn the planet into a police state.
During the New 52 run on Suicide Squad, it eventually turns out that Black Spider is an agent of Basilisk, who allowed himself to be arrested and recruited into the Squad so that he could assassinate Waller.
The most important mole in comic book history is probably Terra of Teen Titans fame. The arc back in the Eighties was so famous it is still known as "The Judas Contract" arc. She is introduced when she apparently rescues the Titans and crushes Slade. It turns out she is working for Slade (and in fact his girlfriend) much later when she leads the Titans into a deathtrap.
According to Knight & Squire by Paul Cornell, DC heroes now refer to this sort of thing as "a Judas contract".
In one week of Wildlife strips, Hanley had Soviet moles in his garden. We meet one of them up close.
In Golden Age Wonder Woman stories, U.S. Army Intelligence often seems to be the service from which CTU inherited its vetting procedures. Steve Trevor goes through a number of secretaries, almost all of whom turn out to be moles working for the bad guys. (Diana Prince didn't work for Trevor, but for his boss, Colonel Darnell. Though come to think of it, Diana herself was a mole, albeit for America's friendly ally, Paradise Island.)
Storm of X-Men Forever was revealed to be a spy for an evil shadow group.
The first cycle of Arthur Benton revolves around a character who was sent as a spy in Germany in 1929, and had to play the perfect Nazi for the following 15 years. It's hard to classify said character as good or bad, and to tell if he is either The Mole or a Reverse Mole.
In Kira Is Justice, Shadow is one in the SIS, while Mr. Williams is partially an unwilling one in the Task Force (though this hadn't been put in play-yet.)
Loyalty is a unique case that features a mole as it's main protagonist. But Sakura is anything but willing.
In Once More with Feeling, Shinji is an unusual mix between mole and Reverse Mole. on one hand, he is feeding intelligence to the Japanese Government about what NERV and SEELE are really up to. On the other hand, given what they ARE up to, and what he is trying saving all humankind -including those he cares for-, you would be hard-pressed to tell he is the bad guy here (and if they knew his motives, it's highly doubtful any character but Gendo and SEELE called him one). He is a good guy pretends to be a bad guy pretending to be a good guy.
In Utopia Unmade, Nisser is one of the soldiers that gains Cure Marine's respect while she's organizing the defense of Sandstorm. Turns out he's actually Cobraja, one of the commanders of the Desert Apostles, and he manages to open Sandstorm's gates to let the Apostles in.
In Mega Man Recut, "The Mega Man in the Moon" reveals that Senator King is this.
The police and FBI suspect the Conduit may have planted a mole within their ranks.
In The Student Prince, Val, the bodyguard, is getting paid to kill Arthur. The surprise may be spoiled for readers who realise that "Val" is short for Valiant.
Films — Animated
Frozen: Prince Hans reveals himself to be The Mole trying to sabotage Princess Anna and her mission.
Heavy Metal 2000: Odin reveals himself as The Mole during the climactic battle, just after the Big Bad has been killed by the heroine.
Monsters, Inc.: Randall Boggs and Mr. Waternoose are in charge of kidnapping children and made up the entire "poisonous human" superstition for the sake of keeping the company up and running to power Monstropolis. The former is only shown as cocky and cruel before The Reveal on how grossly vile he really is, thus less surprising than the latter Mole.
Toy Story 2: The Prospector Stinky Pete sought to aid Al's Toy Barn in making profit, preventing Sheriff Woody from returning home. This Mole changes his ways at the very end.
In Toy Story 3, Lotso is a similar Mole, pushed Up to Eleven of the preceding, given that he puts on even more lovable airs before The Reveal that he's actually far more oppressive. He may have changed his ways at the end as did the preceding, though it is in no way clarified whether he changed at all.
Braveheart played with this trope and its variants; when two characters join Wallace's crew, one appears to be the mole but it turns out to be the other one and the first one saves the hero.
There are two in Carlitos Way. One is revealed right away and is working for the FBI, the other is not revealed until the ending.
Dog Soldiers had a mole, who didn't intend to be the mole originally. The one woman who rescued the soldiers from the Werewolves and tries to help them escape from the surrounded country house is revealed to be a member of the Werewolf family herself. Apparently, it seemed she thought the soldiers knew about the beasts and had come to rescue her (and perhaps cure her) from the Werewolves. However after every escape plan goes wrong, she reveals herself to be one of them, reveals that she had let the rest of the wolves in the house while they were busy and begins changing into one of them herself.
She is promptly shot in the head seconds later.
Dr. No. Miss Taro is an agent of Dr. No who works as a secretary in Government House, passing classified information on to him.
In Indiana Jones and the Last Crusade, Dr. Elsa Schneider is revealed to be working with the Nazis about halfway through the film. She pretended to help Indy in order to obtain Henry Sr.'s grail diary, which could confirm the location of the Grail's resting place. Elsa, however, subverts her role when she purposefully gives Donovan the wrong grail, which eliminates him from the picture, allowing Indy to obtain the true grail and heal his father. In the end, this (questionable) redemption is not enough, as she tries to leave with the grail from the temple. In a Take My Hand moment, she can't keep herself from reaching for the grail below her as she hangs on to Indy above a deep abyss. She ultimately loses her life when her gloved hand slips away and she falls to her death.
Mall Cop: Paul Blart's trainee Veck Sims is the main villain. The trainee is the brainy.
In the movie adaptation of Mission: Impossible, the team leader Jim Phelps, essentially reversing his portrayal for the entire run of the original and second series, which the movie producers weren't even involved in.
No Way Out features a remarkable combination of a mole and a Red Herring Mole. The murder of the mistress (Sean Young) to the Secretary of Defense (Gene Hackman) is blamed on a Soviet mole as a Red Herring to divert attention from the real killer (the Secretary himself). The protagonist (Kevin Costner) must race to find evidence of this before they figure out that he's the one being framed. The twist is that although he didn't kill the girl, Costner really is a Soviet mole.
Reservoir Dogs. After a heist goes wrong, the main characters become paranoid, with Mr Pink repeatedly claiming there has to be a mole. We eventually discover it was Mr Orange.
The Rocky and Bullwinkle film parodies this trope's name. The villans have a mole in the U.S. government that allows them to get information about what the government is doing. The mole is revealed to be a literal mole that is part of the President's Staff.
One of the people in Ronin is not actually "Ronin", and is still working for his/her agency. It's Sam.
In The Heat, Adam, the DEA agent, was Larkin all along.
In The Thieves, Julie is planted on the team by the Hong Kong Police to lead them to the reclusive fence Wei Hong.
Long Wei is informed near the start of Infinity Game that somebody has infected the alternative world with a virus that is causing the game to become more difficult and permanently killing people (originally death in the game meant the player would return unharmed to the real world), so he sets out to find out who it is. It was D.D., infected by the RPG Society.
In Prickly City, Kevin sent Carmen to be a mole in Obama's camp. They sent her to work for Biden. Biden sent her back to Obama to be his mole in Obama's camp.
Used and subverted in CHIKARA. One of the tecnicos had betrayed the others and gave rudoUltraMantis Black the counter to Mike Quackenbush's feared submission finisher the CHIKARA Special to pass on to bigger rudoChris Hero. UltraMantis also hypnotized tecnico Tim Donst into joining his stable the Order of the Neo-Solar Temple. Except, Donst was faking the amnesia, and while one of the rudos he discovered that the traitor of the tecnicos was Shane Storm. Donst told Quackenbush, who attacked Storm before he could pull off a full fledged reveal and betrayal.
After the Zodiac (Brutus Beefcake) left the Dungeon of Doom in February 1996, he was repackaged as The Booty Man (sort of like Billy Gunn's "Mr. Ass" gimmick), now a Face and a Friend of Hogan. Hulk explained that he had sent him into the Dungeon as a "mole." However, it actually DOES make sense when you consider the finish of the War Games match between the Hulkamaniacs (Hogan/Savage/Sting/Luger) and the Dungeon of Doom (Kamala/Shark/Zodiac/Meng) at WCW Fall Brawl 95, September 17, 1995. The Hulkamaniacs won when Hogan forced Zodiac to submit. Hulk had to have Zodiac be the one to submit, since he was the weakest guy on the team, (also because Kamala didn't speak, Meng was/is a legitimate BadassMonster and the Shark was too big) and because it would have looked suspicious if Hulk had fought with the other three guys but left Zodiac alone. The two might have planned for Hogan to not actually apply any pressure when he locked on the submission (so as not to hurt his friend any more than he had to), but for Zodiac to submit anyway (to give his friend Hogan the win against the DOD team). Kind of like a less stupid version of the Fingerpoke Of Doom.
Toward the end of the much-despised Alliance angle where WCW and ECW tried to put WWF out of business, Kurt Angle, who had been a major figure in Team WWF, suddenly joined the Alliance out of nowhere. After Vince tried making the Alliance believe Stone Cold was really a mole planted by him, it is revealed that it was Kurt Angle who was the actual mole, costing the Alliance their main event match, and ending the Alliance for good.
Adventures in Odyssey: The audience was let in fairly early on the fact that Mr. Glossman was a mole, but not on who he was working for.
Paranoia takes this to an extreme; every single character in the game is a traitor working for a different secret society. Some of them (especially Internal Security agents and the Illuminati) infiltrate other secret societies.
And then there's the Wobblies. The Computer heard rumors and sent a Troubleshooter team to investigate, but they'd died out long ago, so the team reported finding nothing— and was executed for failing to follow orders. A dozen or so teams later, one team created the society so they'd have something to investigate. To this day, every single member is an infiltrator.
In Warhammer 40,000, although most Radical Inquisitors are just Cowboy Cops who do their jobs in ways the bosses on Holy Terra wouldn't approve of, there are quite a few extremists who, for various reasons, abuse their Inquisitorial authority to do things that undermine the Imperium's security. Some of them are outright trying to overthrow one or more of the Imperium's ruling bodies.
In The Gentleman Ranker, Lieutenant Harford is a German agent who has been undercover for a decade as a British officer.
Drive: Orla O'Malley is part of La Familia. Nobody in-universe knows this but La Familia.
Jesse in Fans! was revealed to be the mole; his real name is Jesspin, and he is loyal to the time-traveling conquer General Maximilianna. Subverted in that Jesse still exists as a secondary personality within Jesspin and is loyal to AEGIS. When Jesspin told "Jesse" that no one would believe that he wasn't a traitor, "Jesse" answered, "That's what will make this fun. I do my best work in the dark."
Wooster, Gil's loyal companion in Girl Genius, turns out to be a mole from Britain. Unfortunately for him, the one he was spying on knows. That's why he made sure to keep him close, so he can keep an eye on him.
A more dangerous Mole was Rovainen, when it turns out that he is a revenant.
In Mortifer, William Aussek, the newly appointed leader of the local supernatural law enforcement, is revealed to be Magnificent Bastard Joey Von Krause in disguise. A more straight example would be Matthew, who is revealed Post Time Skip to be informing on Joey to Vlad Hynner — Matthew's pissed at Joey for more or less relegating him to desk work, preventing him from venting his Psycho for Hire tendencies. Also, it's revealed that Alyce was working for Vlad the whole time as a double agent.
In an early Sluggy Freelance arc, Riff is revealed to have been acting as a mole for Hereti-Corp since before the series began, albeit unintentionally.
And in the "Phoenix Rising" storyline "Nash Straw" turns out not to be an investigative reporter, but an assassin the Canadian Mafia hired to kill Oasis.
Riff's girlfriend Monica is actually a K'Z'K worshipper sent to spy on the main characters by Chilus.
In the "Research and Development Wars" arc, it is revealed that Sasha has been a Hereti-Corp spy all along.
Ever since Sadako entered the YU+ME: dream storyline, readers were not sure exactly who she was or what her relation to Lia was. When the big Drama Bomb hits, it becomes more apparent who Sadako is.
KateModern season 2 featured two examples of this; first Terry and later Julia.
Dr. Hart in lonelygirl15, who is one of the protagonists for a significant proportion of series 2, before eventually revealing himself to be a villain (but he switches sides during the season finale, "Bloodlines").
A particularly unusual example happened during the live event seen in "Too Dangerous!", in which a group of fans were invited to meet Daniel and Jonas, in person, in San Francisco, and take part in the storyline. Greg Gallows, a popular Big Name Fan of the series, was revealed to be a mole, passing information onto villain Lucy. Gallows went on to appear as an enemy mook in the following story, "Bloodlines".
Sarah was revealed to be a mole in "We're Screwed!"
There's a variation in Survival of the Fittest version 2, where Big Four member Steven Wilson is tasked with scouting Bathurst High School (the other Four were assigned to other schools in the city) to find the best classes to target, and eventually to orchestrate those classes' abductions. They got him in place by forging documents and credentials to establish him as a qualified teacher and administrator, arranged for the previous Bathurst principal to "disappear", and then snuck him in as the new one. He then took over by using his previous military and leadership experience to take care of the administrative details. Ironically, the Bathurst students sealed their own fates by treating him rudely and with no respect, constantly causing trouble, and the two chosen classes were the ones he saw as the worst. Nobody not in the know saw it coming.
Jodene Zalack in Survival of the Fittest version three, who joined a group with the intent of infiltrating them and taking them out. She succeeded in killing Khrysta Lawrence and escaping entirely unharmed. She was planning to do the same to another group before it was decimated by Wade Wilson.
Yu-Gi-Oh! The Abridged Series' Melvin (Yami Marik) was a villain from the get go, but it's taken even further when he turns out to be The Mole for the series itself. He was hired by the CEO of 4Kids (Noah Kaiba) to cancel the show. He succeeded.
The YogscastMinecraft Series has Lysander, who turns out to be a member of the evil cult of Israphel. And he burned down Mistral City while the heroes were investigating what happened to Old_Peculier's father.
Subverted when it turns out Lysander was framed and the person who actually burned down Mistral was a pirate named Jock Fireblast. Played straight though when Skylord_Vitali betrays the Skylords and kills them all.
FBI Agent Robert Hanssen, one of the most damaging moles American counter-intelligence has ever had. Sold information to the USSR that resulted in the deaths of many agents and defectors over a two decade period. At one point, Hanssen was tasked in his counter-intelligence work to find the Soviet mole. He was looking for himself!
His damage wasn't limited to the intelligence community. Hanssen is thought to have leaked information on the FBI's manhunt for Osama bin Laden to Russian handlers. This information ended up on the black market, and eventually into the hands of bin Laden himself. This leak is thought to have helped facilitate 9/11.
Efforts to identify and capture Hanssen were complicated by the fact that he and Aldrich Ames (below), a Russian mole in the CIA, were operating at the same time and in some cases leaked the same information.
Edward Snowden, in spite of what Americans "found out" about domestic NSA spying (most of the more-informed already knew and were not the least bit surprised), now has been found to probably not have been working by himself the entire time. He had defected to leftists overseas while still working for the NSA, just waiting to fully leave at the right time. Of course, those sympathetic to said forces praise Snowden as a hero, though they refuse (because they can't) to explain how revealing the details of the development of Stuxnet to foreign enemies is helpful to the American people.
Aldrich Hazen Ames, one of the most notorious double agents in CIA history. Received approximately $4.6 million from the Soviets for selling out several CIA sources and operations to them from the 80s until his capture in 1994. His actions as a Soviet mole were so shocking and poignant that a movie was made about him, Aldrich Ames: Traitor Within, and he's been referenced in several espionage stories since his discovery. Also infamous for beating the regular CIA polygraph tests by being very calm.
Several of the Cambridge Five in the UK could be classed as this, but the most infamous would probably be Kim Philby who, as a long-term spy for the Soviet Union within MI6, at one point became head of Section IX: tasked with counter-espionage against the USSR; at another point he was MI6's liason with the CIA.
Mark Zborowski, yet another Soviet mole. He wormed his way into Trotsky's circle and possibly assisted in the death of Trotsky's son.
Anna Chapman, the gorgeous hot chick, turned out to be a spy for the Russians. Along with nine other nameless guys, by the way, whom the media didn't care about.
When the British anti-capitalistic left-wing organisation Lordon Greenpeace was involved the so-called "McLibel case" against McDonald's, it was estimated that up to one half of the members of the organisation was moles both planted by the British police and McDonald's itself.