Many of Le Carre's novels involve moles in one way or another, and the main character of A Perfect Spy is a mole.
In fact most Stale Beer flavour Spy Fiction features moles and mole hunts as central plot points. The Cambridge Five and Aldrich Ames left pretty deep impressions on the genre.
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.
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 Ben Counter's Warhammer 40,000 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 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 Gaunts 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 Heel-Face 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 Heel-Face 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.