24: This show has probably the most famous example of this. Over the course of eight seasons, there have been fifteen named and confirmed moles, not counting the hundreds of unnamed ones in Day 7. This figure also doesn't include double and triple moles. Amazingly, even by the eighth season, the characters are still astounded when a mole within CTU is uncovered. This has prompted many fans to suggest that Jack Bauer needs to have a long talk with CTU's director of Human Resources. Not just CTU itself, every agency in the series is plagued by numerous moles.
The Adventure Game: After appearing as a contestant on the first series, Lesley Judd then appeared as The Mole on later series, culminating in a puzzle where the other contestants had to avoid finishing on the same square as her, otherwise they would be eliminated.
Agents of S.H.I.E.L.D. reveals multiple moles in "Turn, Turn, Turn": HYDRA has so thoroughly infiltrated S.H.I.E.L.D. that they are able to stage a coup, capturing multiple S.H.I.E.L.D. facilities. In addition, Agent Garrett turns out to be the Clairvoyant and a HYDRA operative, and Agent Ward turns out to be his right-hand man. Later in Season 2 Episode 3 "Making Friends and Influencing People" it is revealed Agent Simmons is undercover in HYDRA, leaking their projects to Coulson and in Episode 5 "A Hen In The Wolf House" Bobbi Morse A.K.A Mockingbird, Head of Security for HYDRA is also a mole...put in charge of finding moles.
Angel: Cordelia is like this in Season 4, although it isn't the real Cordelia as her body is being used by an antagonist higher power of ambiguous morality.
Arrested Development: Spoofed, when Tobias is asked to be a mole for the CIA; he think it's a casting agency, and assumes they want him to put on a mole costume.
Ashes to Ashes: It is revealed near the end of season 2 that Chris has been blackmailed into being a mole. He is however not a bad guy, so he redeems himself promptly with a Face-Heel Turn.
The Assets is the true story of Aldrich Ames, a CIA agent who was a mole for the KGB for years.
At the end of the first season, Garibaldi uncovers a plot to assassinate the president of the Earth Alliance. Before he can deliver a warning, he is shot in the back by his aide Jack.
In "Divided Loyalties", Lyta Alexander delivers a warning that someone on the station has a deep-cover personality implanted by Psi Corps. It turns out to be Talia Winters.
Battlestar Galactica (Reimagined): Played with in the 2000s. From the beginning of the first season the audience is aware that Boomer is a Cylon, although the crew of the ship, and Boomer herself, are not. The season arc features her struggling with self-doubt over whether or not she's human, attempting suicide, and ultimately learning that she is in fact a Cylon. In the season finale, she seemingly sides against her kind and sets off a nuke destroying a Base Star full of other copies of her, and at that moment the Wham hits; as Commander Adama is meeting her in CIC and praising her for a job well done, she draws her sidearm and shoots him twice, point blank, in the chest. The reveal of several other characters in the season three finale includes two significant moles, as well as two lower tier individuals. Not really moles though — their presence in the fleet turns out to be more like a punishment — or a joke.
Blackadder Goes Forth: One episode has Blackadder look for a mole within the military hospital. He takes the opportunity to torture...I mean interrogate Darling for kicks, and gets cozy with the hospital nurse, while a man with an obvious German accent is a patient in the hospital. Come to find out in the conclusion, though, the nurse was the actual mole, and the 'German spy' was, to Darling's embarrassment, a British mole who picked up an accent during his time in Germany. Then the Twist Ending reveals that George was inadvertently the mole, writing letters to his German uncle.
Bones: Zack Addy is one for the Gormagon. He comes back occasionally, though, because he's a freakin' genius and nobody else can figure out the killer.
Jenny was sent to Sunnydale to keep an eye on Angel.
The Closer: In the final season, a leak in Chief Brenda Leigh Johnson's department traces back to Lieutenant Gabriel's girlfriend Ann. Goldman hired her to cozy up to Gabriel for inside information about the LAPD and Brenda's cases especially. Gabriel is legally cleared of wrongdoing, since everything he shared with Ann was said in confidence. He's still heavily scorned by members of the team for his accidental role in the leak.
"The Web of Fear" concerns the fact that one character in the group is working for the Great Intelligence. Oddly for anyone who knows anything about Doctor Who, the character clearly intended to be the primary suspect for most of the story is Colonel Lethbridge-Stewart. (The novelisation alters this by clearing him of suspicion early on.) The Genre Savvy viewer's primary suspect is probably Chorley. The actual suspect turns out to be Arnold, a Mauve Shirt who got killed in an earlier episode and is still moving around as a possessed corpse.
In the episode "The Runaway Bride", Lance - the fiance of the eponymous bride - is revealed to be working for the sinister Queen of the Racnoss. And in "The Last of the Time Lords", a scientist employed by Martha turns her over to The Master. In a minor subversion in the latter example, however, Martha's actually counting on her doing so as part of her plan.
In a heroic example, the alternate-universe Pete Tyler is revealed to be a spy inside Cybus Industries, anonymously sending information to the Preachers.
The character of Vislor Turlough is initially introduced as a mole character who orchestrates his way into becoming one of the Fifth Doctor's companions under orders from the Black Guardian to kill him, but eventually does a Heel-Face Turn and defies the Guardian and goes on to become a loyal companion for the rest of his time on the show.
Dollhouse: The early episodes set up that there's a spy somewhere in the House, eventually revealing it to be head of security Dominic. Notable in how the character was practically the only one fans hadn't suggested The Mole to be...because it was such an obvious choice, everyone assumed that it ruled them out. Oh, Joss Whedon, you insane genius. In the final episodes it is revealed that in fact Boyd, a trusted figure in Adelle's house, was the one in charge of Rossum Corporation.
In Dominion, the humans now face a serious threat of this from the Powers, who don't need to possess human hosts, and can thereby get past the angelic detection equipment. And then there's the Black Acolytes, the cult that worships Gabriel, and are far reached enough that one of them is William Whele, leader of the Church of the Savior and son of the second most powerful person in Vega.
Firefly: Yolanda/Saffron/Bridget made a living out of being The Mole. She was introduced as an innocent and submissive young woman. She claimed she's a reward as wife for their captain because her people couldn't pay them in a standard way while in fact she's a trained companion and criminal mastermind who tried to kill the crew in order to sell their ship. She also ratted out her husband who loved her deeply and thought she was kidnapped from him.
Glee: Quinn, Santana and Brittany, the three Cheerios who join Glee Club, are secretly spying for Cheerios coach Sue Sylvester, who is trying to bring down the club. As the series goes on, though, and Quinn's popularity and membership in the Cheerios are destroyed by her pregnancy, this gradually changes.
Greek: Jen K is a mole for the school newspaper, and puts a dent in the entire Greek system with her article. Apropos that Jen K is played by Jessica Rose of lonelygirl15 fame (see below).
Sailor Wolfe seemed to be an ordinary seaman who joined HMS Hotspur by mere chance because he just wanted to serve in the Royal British Navy. He's an Irish rebel who collaborates with Napoleon Bonaparte, trying to liberate Ireland from the Brits by invasion and war.
Captain Hammond was mentioned by name in several episodes and appeared in all three instalments, but he never looked to be a significant character, other than he was a rather famous figure in the Navy and a Hanging Judge during a court-martial in "Retribution". In "Loaylty", it's revealed that he was secretly working for Irish rebels his whole life.
In "War Cries", the boy, his sister who the Marine was dating, and their mom were all sleeper agents for the Shining Path, and weren't even related to each other.
In "Brig Break", Gunnery Sergeant Gentry.
In "Ares", Lieutenant Commander Gino Campisano is the senior weapons officer running the eponymous computerized weapons system onboard the destroyer: and suddenly, while off the North Korean coast, it starts to go crazy, operating without human input, and allowing no vessels other than ships to approach it. What no one knows is that Campisano is a North Korean mole, planted in the United States many years ago.
Leo, one of the new guys at surveillance Ed hired in season 2, is revealed to be working together with a group of card counters.
Adam, an employee remotely overseeing the card games in "Hit Me" is revealed to be sending electronic signals to a player.
LOST: Seconds after Flight 815 crashed, Ben dispatched minions to infiltrate the survivors. They later turn out to be Ethan in the main group and Goodwin in the Tailies. In season two, Michael is forced to act as a mole. In season three, an elaborate ruse is utilized to let Juliet infiltrate the survivors, but she turns pretty quickly.
MacGyver: In "The Enemy Within", Mac must discover the identity of a mole within the DXS who has caused the death of four agents.
Merlin: Morgana was The Mole for most of season 3, and now Agravaine has taken over the role, working for Morgana
The Mole: This TV-program is the Reality Show version of this trope. The contestants engage in various challenges, and the better they do, the more money goes in the winning pot; at the end, the winner gets the pot, and the Mole gets the rest of the prize fund as a measure of how well they screwed things up. The contestants are also periodically quizzed about the Mole's identity and actions, with the poorest scorer eliminated. Played with: as a metagame strategy, non-Mole contestants also screw up on purpose, to fool others into thinking they're the Mole and thus do poorly on the quizzes. Sure, it decreases the winner's take, but it increases your chance of being the winner.
Neverwhere: Used to good effect, where the Big Bad's Dragons inform the heroes that there is a traitor among them. The viewers are led to believe that it will turn out to be the Marquis de Carabas, and it is made clear that the heroes believe this as well, but it's really the bodyguard, Hunter.
Nikita: Inverted Trope where the character of Alex is set up to be the mole from the very start, and we see it all from her point of view. She remains the mole for the entirety of season 1. There is even a Was It All a Lie? moment coming from a more minor character, Thom, directed at the main character of Alex mid-way through the season.
NUMB3RS: In the season 3 finale, FBI agent Colby Granger was revealed to be a spy for the Chinese. But in the premiere of season 4, it was shown that he was a double agent the whole time.
Nate Walker/Jason Neville is revealed to be a militia spy as soon as they get to Miles in the pilot episode. In episode 5, it is revealed that he is Tom Neville's son.
In episode 8, Mia Clayton, Nora's sister, is not only this, but also a Bounty Hunter who captured Nora's fellow rebels and was working for that Sergeant Will Strausser. Nora was so disgusted that she abandoned her, even though they had made a promise to look out for each other.
In episode 9, Joseph Wheatley, ostensibly of the rebels (possibly going by "Captain Burke"). In fact, he's been a militia spy for some time.
Episode 17 had Miles quickly realizing that a mole has tipped off Monroe to the Resistance's whereabouts. Episode 18 has Miles trying to find out the mole's identity, and Jason Neville is the prime suspect. However, it turns out to actually have been Jim Hudson.
Robin Hood: A series 2 subplot in the 2006 BBC adaption features Allan a Dale working as an informant for Guy of Gisborne, resulting in his exile from Robin's gang and the end of all his friendships when his treachery is unmasked. He is technically a good guy, so he also occasionally acts as a Reverse Mole, though this is much more rare until the season finale, in which he deliberately contradicts Guy's orders in a semi-suicidal bid to save the gang's lives and rejoins the band.
Uses this with Michael Eddington. Originally a by-the-book secondary character who is more loyal to Starfleet than the rest of the cast, Eddington is eventually revealed to be a Mole for the rebellious Maquis.
There's the time Doctor Bashir was revealed to have been a Changeling impostor for the last several episodes.
Malcolm Reed works for an early incarnation of Section 31, while reporter Gannet turns out to be working for Starfleet Intelligence and Ensign Masaro for radical Earth group Terra Prime. Reed, at least, wasn't all too happy about betraying his commanding officer, and when push came to shove, he stood by Archer. He is one of the few characters of whom this can be said.
Ruby turned out to be The Mole who really wanted Sam to kill Lilith, thereby releasing Lucifer from his prison at the end of season 4. Like Ruby being a mole was surprising to anyone except Sam himself.
Uriel is revealed to be a mole killing angels in "On the Head of a Pin".
The Vampire Diaries: Damon starts out as a mole in the founder's council. But soon he becomes an actual member and turns out to be the most useful.
Whodunnit" Is very similar to the mole in this respect, as one of the guests in secretly the killer
The Wild Wild West: The episode "The Night of the Bleak Island". West's old friend Sir Nigel Scott turns out to be the Big Bad.
During Season 2, the investigation into the Greek's syndicate is sabotaged at several points along the way by leaks from an FBI agent on his payroll.
Agent Fitzhugh's apology to Daniels suggests that the leaking agent isn't corrupt, but another product of the FBI emphasizing counter terrorism over everything else. The Greek is protected from investigation by the FBI in exchange for counter terrorism intel.
Has this trope all over the place, Played With and from various points of view.
At the beginning, Mulder doesn't trust Scully. She's officially assigned to work with him, and everyone knows it's really to debunk his work. He thinks she might be connected with the conspirators, but she's honest and only submits her reports to their supervisors. Her loyalty soon belongs to Mulder completely, and he knows it.
It pops up from time to time that Mulder and Scully's direct supervisor, AD Walter Skinner, might be dirty and collaborate with the shady conspirators. Nope, he's allright and one of Mulder and Scully's strongest allies.
From the conspirators' point of view, Mulder's Mysterious Informants are The Moles who rat them out, trying to ruin their cause.
Deep Throat was involved with them and claimed that he wanted to atone for his deeds, therefore he helped Mulder in his quest for exposing the truth.
Mr. X was very pragmatic. He never made it a secret that he does what's best for him. He worked for the Cancer Man, and was informing Mulder behind his back.
Marita Covarrubias played it on both side. She was helping Muldler, and telling on him to the conspirators
Scully's replacement for a brief amount of time in season 2, Alex Krycek. He was an FBI agent assigned to work with Mulder when The X-Files division as shut down and Scully was sent back to teach at the FBI Academy. Mulder never fully trusted him, but it was a bit of a surprise when he was revealed to be telling on Mulder to the arc villain, the Cigarette-Smoking Man.
In The Movie (The X-Files: Fight the Future), Well-Manicured Man is revealed to be one. The conspiracy group are in fact Well-intentioned Extremists, and he gives Mulder vital information, as well as a vaccine to save Scully.
Agenta Fowley and Spender, a pair of Agents put on the X-Files cases in season 6. Spender was more unassuming, never caring and happy to be destroying the files and informing the conspirators. But his partner Diana Fowley presented herself as Mulder's ex-girlfriend who still likes him and who are Birds of a Feather, like minds that should support each other and similar B.S. Mulder, to his credit, said that Scully's scientific approach had saved him and kept him honest. She collaborates with the Cancer Man and has Mulder subjected to horrific disease and treatment/experiment. However, she ultimately helps Scully to save him.