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.
Runaways had a particularly shocking Mole in its first arc.
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.
In one week of Wildlife strips, Hanley had Soviet moles in his garden. We meet one of them up close.
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.
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.)
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".
Storm of X Men Forever was revealed to be a spy for an evil shadow group.
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.
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.
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.
Loyalty is a unique case that features a mole as it's main protagonist. But Sakura is anything but willing.
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.)
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 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.
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.
No Way Out features a remarkable combination of a mole and a Red Herring Mole. The murder of the Defense Secretary's mistress 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 mole.
Stalag 17 involves one of these in a German POW camp during WW 2. It turns out to be someone other than who everyone assumes it to be.
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.
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.
Becky in Sin City ends up ratting the Old Town girls out to the mob.
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.
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 (Faces) had betrayed the others and taught rudo (Heel) UltraMantis Black the counter to Mike Quackenbush's feared submission finisher the Chikara Special. 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.
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.
In Warhammer 40000, 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 Sluggy Freelance, 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.
And Riff's girlfriend Monica is actually a K'Z'K worshipper sent to spy on the main characters by Chilus.
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.
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.
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."
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!
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 MI 6, at one point became head of Section IX: tasked with counter-espionage against the USSR; at another point he was MI 6's liason with the CIA.
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 espionange stories since his discovery. Also infamous for beating the regular CIA polygraph tests by being very calm.
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.