In Dan Abnett's Brothers of the Snake, the Space Marine Khiron killed another and claimed that he was warp-tainted, but there was no evidence. Another Marine, Priad, talked to him to learn what he could and discovered the daemon had possessed another Marine, who was trying to get Khiton killed.
In William King's Space Wolf novel Ragnor's Claw, Gul.
In Dead Sky Black Sun, Obax Zagayo. Honsou scorns him not for the treachery but for thinking he could conceal it.
In Ben Counter's novel Hammer of Daemons, Alaric feeds some information to an eldar gladiator. After he leads a Gladiator Revolt, Alaric prevents the eldar from getting on the ship: his captor had learned the information, and it being false, he could only have learned it from the eldar. Whereupon Alaric accuses him of having betrayed the previous Gladiator Revolt — which had been crushed, and games had been held to celebrate that victory, and those games had killed Alaric's friend and fellow Grey Knight. He kills the eldar.
In President's Vampire the Vice President, Wyman is Shadow Company's mole in the White House, sharing information in exchange for becoming the President.
Ice Station: Snake, Montanna and Sarah Hensliegh are members of the Intelligence Convergence Group, dedicated to covering up scientific breakthroughs by making sure only they know about it by killing anyone else who does.
Temple: Nash, Lauren and Troy are only pretending to be DARPA, so they can steal the idol for the army's use.
Uli "Craterface" Becker is a German agent pretending to be a Nazi.
Martin Race is a DARPA employee secretly helping the army.
Troy is also working for a terrorist group.
Area 7: Botha and Echo Unit are both trying to steal the perfect vaccine.
In Bill Granger's The British Cross, fourth in The November Man book series, it is revealed that a russian spy has been working as a mole in the British Secret Services.
The Harry Potter books continually go back and forth with Snape. The main characters have thought that he was every single one of the Mole examples listed above at one point or another, regardless of what he actually is. He is a triple agent, appearing as a double-agent to both sides, but actually on the side of the Order all along, motivated by his love for the late Lily Potter.
Also, Peter was the Mole in the Marauders. He was spying for Voldemort and was the one who gave up James and Lily Potter's location and then he framed Sirius for it, to boot.
In Dan Abnett's Gaunt's Ghosts novel Blood Pact, Gaunt deduces very early that they can trust no one because of the way the raid was carried out. In the end, the Mole is identified as Inquisitor Rime. Also, Xomat turns out to be the inside man for Csoni's planned assault on Urbano's parlour.
In The Silmarillion, Maeglin is the lord of the house of the Mole. Because he's "great among quarrymen and a chief of the delvers after ore." And, possibly, because he betrays the location of the hidden city of Gondolin to Morgoth.
Wellington Yueh in Dune, betrayer of House Atreides.
Dain in the first Deltora Quest series was a pretty darn good Mole. He's a Grade 3 Ol, who's known for perfect transformation, and disguised himself as the (fake) heir with a good cover story and infiltrated the La Résistance's organisation as a spy. He managed to fool everyone else even when the Seven Tribes renewed the vow and the Belt seemly pointed him as the heir, when it actually points to Lief.
In Peter F. Hamilton's Pandora's Star/Judas Unchained novels, the human protagonists come to realize that their society's government is riddled with Brainwashed Moles controlled by the alien Starflyer.
Recurring trope in Dale Brown books. In Flight of the Old Dog one of these allows for the critical damaging of a space station, gives away two stealth bombers en route to the plot-critical Soviet SuperscienceWave-Motion Gun and forces the eponymous Airstrike Impossible to get going while You Can Barely Stand... and the whack-a-mole subplot is effectively nonexistent. Day of the Cheetah is centred on one of these getting his hands on a Super PrototypeCool Plane. Act of War has National Security Adviser Chamberlain turn out to be the one giving information away to the terrorists. It's Michael Fitzgerald in A Time for Patriots, though he does a HeelFace Turn.
Gertrud Becker in The Chalet School in Exile, aka Gertrude Beck, a Nazi spy sent to infiltrate the Chalet School and gather information. However, she finds out very little after the older girls realize there's something odd about the questions she asks and warn other girls to keep quiet, and she ends up having a HeelFace Turn after running away and being rescued by some French sailors.
The Black Ajah consists of a number of moles operating in the other seven Ajah in the White Tower in the Wheel of Time series.
In Bad Monkeys, Jane Charlotte is revealed in the last 5 pages of the book to be a mole in an unnamed organization devoted to fighting evil. This revelation makes her account of how she got in the organization that she tells to her psychiatrist (and thus the entire book) only half true.
Linda Lane in Septimus Heap. Without her spying on the Heaps and gaining their trust, Jenna would have never been discovered.
In the historical novel Wings of Dawn: In order of being revealed: Sir William. Waleran. Isabelle. Geoffrey. Katherine. Waleran. Gervaise. Lord Baldwin. Waleran. Reason being, quite a lot of them were spying on each other before Thomas got involved. (Yes, one of those is duplicated for a reason.)
In Wen Spencer's Tinker, Sparrow. In Wolf Who Rules, Tinker is able to assure the elves that Tommy is not this because he had information, which he obviously did not pass on.
In Lois McMaster Bujold's The Warrior's Apprentice, Tung explains that one of his men did not defect to Miles's forces because he was a Barrayan spy. Tung actually likes spies, as long as the information is unlikely to harm him, because they're reliable, but this one had to spy on the other fleet, so they parted ways.
In Tom Kratman's Caliphate, Ling is a Chinese agent sent into a brothel where Petra was working. She also becomes a big sister figure for Petra and aids her in coping with living.
Trapped on Draconica: Taurok placed Lydia inside Daniar's group to mine intel, but Lydia herself was unaware of this because she's five years old. As far as she knows, she's helping her grandfather with his work.
In A Deeper Blue, several Islamics in ordinary positions are used to assist the VX attack on Florida, although one of them only does so at gunpoint once he discovers what he's being told to actually do.
Two of Bond's allies turn out to be in league with the Nazi terrorists in Icebreaker. The third also seems to be one at first, but is revealed to be a Reverse Mole in the final chapter.
The plot of No Deals, Mr. Bond concerns about Bond trying to help defectors from East Germany, capturing an KGB official and finding the traitor among a now-defunct Honey Trap operation.
It turns out in Death Is Forever that the agent-network that Bond is investigating had two moles in it feeding information for the Big Bad. The other turns out be a Reverse Mole looking for the actual mole.
In High Time to Kill, someone in the SIS feeds information to the Union about Bond's movements. Tragically, it turns out to be Bond's girlfriend Helena Marksbury, who is being forced to do so, and who is killed after she outlives her usefulness.
Juliette, the nurse that helps Grimaldi escape the hospital and fake a carjacking
Tom Drabowski, the FBI Agent brought in to "investigate" the carjacking and help Grimaldi escape police surveillance
Sebastian/Jonathan in City of Glass. He was the reason Valentine knew what Jace's group was about to do. He killed the real Sebastian Verlac and posed as the Penhallows' cousin in order to get information.
In The Dinosaur Lords, Longeau, Karyl's loudest opponent in the Garden's Council, is actually a mole of Brokenheart knights, who seek to destroy the Garden. He claims he does that to avoid Fate Worse than Death.
In The Girl from the Miracles District, it eventually turns out that one of the Bears is spying on the rest and at one point puts them into Forced Sleep so that the villains can kill Nikita. As he explains in his Motive Rant, he never intended to have the Bears hurt and only wants Nikita dead because he holds her responsible for his father's death.
Played With in River of Teeth. After they are attacked by a feral hippo outside of the Harriet, Archie proposes the possibility to Adelia that the crew may have a mole among them. The natural suspect to turn to is Cal Hotchkiss, since he'd been working for Travers until recently and could have been threatened by Travers into providing him with information. But it turns out that Adelia Reyes has been the mole all along, having been payed by Travers to not only reveal the crews plans but also to kill them all should the need arise.
In A New Kind of War by Anthony Price, Frederick Clinton's counter-intelligence unit has the kind of trouble that has to mean there's a mole; a particularly troubling situation in that all his officers were hand-picked and have passed rigorous background checks. It turns out to be none of the officers, but Colonel Colbourne's trusted assistant, Sergeant Levin.
Near the climax of Dreadnought!, Piper's friend Merete reveals that she is one of Rittenhouse's loyalists, and Piper realizes that certain things that happened during the book are due to Merete subtlely tipping off Rittenhouse and his people. However, Piper is able to talk Merete out of her loyalty to Rittenhouse through a combination of helping her realize that he's manipulated her from the start and the obvious truth of Rittenhouse and his cronies trying to destroy the ship they're on. The clincher is when an attack causes an explosion that badly injures Merete just as she's about to hand Piper her phaser.
Gatling: In Border War, part of Gatling's mission becomes uncovering the British agent planted within the metis ranks.
In Star Wars: Razor's Edge, one of Leia's crew is an Imperial agent, having leaked coordinates for where her ship, the Gamble, would be receiving a transmission to the Empire. When the Gamble escapes the resulting ambush, he spends the rest of the story looking for another opportunity to bring the Empire down on them. Leia and Han would have a much tougher time of things if he was better at his job.
The Traveler's Gate: Leah was sent to Myria to search for the prophesized Elysian Traveler. Or rather, she was sent out to live on her own because that's a royal tradition, and they decided to have her look for the Elysian at the same time just in case he turned out to be real. Leah actually identified Alin in her first few hours in the village, but eventually dismissed him because he wasn't having any contact with the rebels. The truth is he hadn't come into his powers yet and was completely unaware of his destiny; Leah is rather embarrassed when she finds out how much she messed up.
In the Xandri Corelel novel Failure to Communicate, the ambassador Marco Antilles turns out to be a member of the Last Hope for Humanity, trying to sabotage the alliance between the humans and the Anmerilli.