Anderson: Psi-Division: In "Half-Life", there's a resistance movement against the increasingly murderous rule of old Deadworld's judges. It includes a man named Fuego, who lures them into an ambush before revealing himself to be an undercover Judge working for De'ath. It turns out that this is the human who became Judge Fire.
Necronauts: H.P. Lovecraft has been recruited by the Sleepers in the Void to spy on Houdini and his allies. He redeems himself when they break him free of their influence.
Arthur Benton: The first cycle 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.
Royal Williams joins Pyramid to get information about the man who killed his parents. He feeds information to his brother Charles, who forwards it to the authorities as needed.
Lord Saampa was chosen by the Oubor to lead its cult, but he keeps them busy with useless rituals so they don't hurt innocents, even as he tries to resist its influence.
Black Dynamite: One of The Man's bodyguards is revealed to be part of the rebel alliance, and helps Black Dynamite escape from Guantanamo Bay.
Clean Room: A member of Astrid's inner circle is recruited to pass information to the demons and sabotage the Mueller organization as appropriate.
Danger Girl: Natalia Kassle is introduced as one of the original members of the team. However, she is revealed to be a member of the Hammer Empire in #5 after having faked her death in #4.
Double Duck: After her Heel–Face Turn, Kay K works for the Agency and becomes the mole into the Organization.
Fables: The comic series 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.
Gene Dogs: In the Marvel UK series, team member Panther - a mole for recurring villains Mys-Tech - is promptly killed in the first issue. Mission control knew she was a mole, but not whether she was working alone (so hadn’t told the rest of the team). Her replacement’s first job is to check the loyalty of the survivors.
Green Lantern: In The Green Lantern, the Guardians send Hal Jordan undercover with the Blackstars to find one of these within the Green Lantern Corps.
Iron Man: Tony Stark'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.)
Legends of the Dead Earth: In Legion of Super-Heroes Annual #7, it turns out that the Durlan Legionnaires Shape and Shift are conspiring with their people to prevent the re-establishment of the United Planets.
Millennium (1988): Part of the premise of DC's 1988 Crisis Crossover 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.
The Multiversity: The residents of Earth-42 serve as this for the Empty Hand, acting as its eyes and ears.
Perfect Dark: The Perfect Dark: Janus Tears comic book revolves about Joanna Dark haunting a mole in the Carrington Institute.
Revival: One major character in addition to their day job is feeding information to the CIA.
Runaways: The Runaways had a Mole in the team as one of the running threads in its first 18-issue arc, leading to a particularly shocking reveal:
Robin (1993): The cold assassin that Dodge brought on as part of his villain team up to take down Robin turns out to be Ravager having the time of her life messing with them while keeping Robin and the Teen Titans appraised of their plans. She's downright gleeful when the time comes to take them down and she gets to suddenly attack her "allies" and reveal her identity.
Secret Invasion (2008): Part of the premise was that various characters had been replaced by the shapeshifting Skrulls. Unlike DC's Millennium (1988), which shared the same general premis, Marvel did this 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.
Secret Wars (1984): Klaw sabotages Doctor Doom's godlike powers subconsciously, because the Beyonder has taken him over.
Sherwood, Texas: Rob and the Jesters plant Much as a mole inside the Nobles biker gang.
Sonic the Hedgehog (Archie Comics): A retcon and a bit of Arc Welding are eventually applied so that Geoffrey St. John's apparent Face–Heel Turn turns out to actually be this, stating that he's really been working for Ixis Naugus since before either of them were even introduced.
Sonic the Hedgehog (IDW): During the Misadventures arc, Clutch forms a Legion of Doom with several other villains not associated with Eggman, and sends three of them to infiltrate the Restoration in order to help him bring it down from within — first, Mimic takes on the identity of "Duo the Cat" to join the heroes and volunteers to join the Neo-Diamond Cutters, then Surge and Kit present themselves as having had a change of heart, taking any heat off of Mimic as Sonic and the others are too busy watching them for any hints of betrayal.
Spider-Woman: The Shroud has been undercover as a supervillain since the '80s, even going so far as to form the Night Shift, a team of supervillains with no idea their boss is working to destroy the underworld from within. Werewolf by Night was also a member of the team, and since he was faking a Face–Heel Turn for the role (especially since a former foe of his, Tatterdemalion, was also on the team), was the only member of the team the Shroud trusted with his secret. When the Shroud left the Night Shift, Werewolf left as well.
Squadron Supreme: Several are used in the limited series as part of a plot to stop the heroes' efforts to turn the planet into a police state.
Dulac is revealed to be a Vong agent who has spent decades pretending to be a human in order to weaken resistance from the inside.
The Imperial ambassador is likewise a Vong agent sent to keep the Republic leadership distracted from the invasion.
Star Wars (Marvel 1977) had Shira Brie, a Force-sensitive Imperial spy who infiltrated the Rebellion with the goal of either killing Luke Skywalker or ruining his good name. She briefly succeeded in the latter by getting close to Luke, then tricking him into shooting down her TIE Fighter and making everyone believe he had killed a champion of the Rebellion... until he found records proving her true identity. She was then rescued by Darth Vader and became one of the Emperor's Hands (alongside Mara Jade Skywalker), taking the name Lumiya.
Star Wars (Marvel 2015): Queen Trios of Shu-Toran makes contact with Leia during the Ashes of Jedha arc and reveals she's willing to act as an informant and agent for the Rebellion within the Empire. She proves her worth during the following Mutiny on Mon Cala arc, being key to helping the Rebels get what they need to get the titular mutiny kicked off. Then the end of that arc's last issue reveals that she's actually been working for Vader the whole time, manipulating the Rebellion into trusting her so she could sabotage their fleet and sell out their headquarters to the Imperials. This plays out during the following Hope Dies arc, with Trios' deception being revealed and quickly earning her a place as Leia's new Arch-Enemy.
Suicide Squad: During the New 52 run, 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.
In Who is Superwoman?, the titular villain infiltrates the city of Kandor and poses as a Kryptonian in order to spy on the House of El, per General Sam Lane's orders.
In The Black Ring, Robot "Lois" is supposedly working for Lex Luthor, but in reality is an agent of Brainiac. Nevertheless, Luthor anticipated this and planned accordingly.
In The Girl with the X-Ray Mind, Lena Thorul joins a criminal gang called the Bank Busters; then she takes them down right when they are robbing a bank, and reveals that was her plan all along.
In Action Comics #317, Supergirl believes her friend Lena's boyfriend Jeff Colby is an enemy spy. Later she finds out that Jeff was really working with the FBI and trying to trap a spy ring.
Teen Titans: Terra. The arc back in The '80s was so famous it is still known as The Judas Contract arc. She is introduced when she apparently rescues the Titans and crushes Deathstroke. It turns out she is working for Deathstroke (and in fact his girlfriend) much later when she leads the Titans into a deathtrap. According to Knight and Squire by Paul Cornell, DC heroes now refer to this sort of thing as "a Judas contract".
Tintin: Frank Wolff, Calculus's assistant in the album Destination Moon/Explorers on the Moon.
Wonder WomanVol. 1: In Golden Age 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.)
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.
In Extermination (2018), the French twins rescued by the Blue team turn out to be working for Ahab.
Storm of X-Men Forever was revealed to be a spy for an evil shadow group.
In Wolverines, Mystique is secretly working at cross-purposes to the rest of the group, using information left to her by Destiny to use them for her own ends.
As soon as Chris Claremont returned to writing the series, he revealed that Tessa (aka Sage) had been a Reverse Mole for the X-Men... for the first 20 years of her editorial history! Previously, she seemed to just be the telepathic secretary of the Hellfire Club's Sebastian Shaw.
Y: The Last Man: The Australian naval officer and spy Rose Copen forms a lesbian relationship with Dr Allison Mann so she can accompany her and thus keep tabs on the last man on Earth only to fall in love with Allison for real.
