The revelation that sentient Titans are in fact "humans in Titan flesh" becomes a source of Paranoia Fuel. However, the eventual discoveries that Annie, Bertolt, and Team Dad Reiner are spies sent to infiltrate the human ranks is both shocking and a punch to the gut for the characters and the audience. Even worse, Bertolt and Reiner are the Colossal Titan and the Armored Titan, respectively... and therefore responsible for a good percent of the death in the series thus far.
Eren Kruger is also a mole: he infiltrated the military by faking his identity and then leaked information to the underground resistance movementGrisha Yeager was a part of. Another mole in the series could arguably be Zeke, Grisha's son, who turned his parents in for being part of said resistance, despite their insistence that he's their only hope at restoring the Eldian empire to its former glory. Attack on Titan likes this trope a lot.
Bloody Cross: Nao appears to be an ally and talks about how much they hate villains, but it's all an act and they're actually a mole for Satsuki.
In the Blue Exorcist manga, Mephisto reveals that there is a spy in the Esquire class... but nobody expected it to be Shima Renzou.
In Brave10, Anastasia works for Hanzo and has been gathering intel the whole time.
In Corrector Yui, once Haruna joins the team, it isn't long before she starts using her mind-control voice (which only Yui, as a human, can resist) to make the others pick each other off. Haruna herself doesn't know it and then she turns out to be Brainwashed and Crazy (she's even turned into a Dark Magical Girl), but the guy controlling her actually made it subtle.
You Takami spies on Ganta in Deadman Wonderland in exchange for the over 90 million "cast points" (DW money) he saved up to buy his sister's freedom. Ironically, not only does Ganta figures out You's just using him and doesn't care but his sister really does deserve to be imprisoned.
Technically, Light Yagami becomes a kind of mole in Death Note when L gets him onto the team and again when L dies, and the others get him to lead the detectives.
Misa is also frequently a mole, sometimes several layers deep.
Subverted in Detective School Q. Everyone thinksTatsumi Hongou is the mole from Meiousei -aka the Pluto Organization- and that he arranged Morihiko Dan's kidnapping, but Tatsumi himself confronts the Q section people and calmly says he knows they don't trust him, that he's not the mole they're searching for, and that they should team up and help him find said mole. It turns out that the mole is Shino Katagiri. Or better said, a Meiousei agent impersonating her, as the real Shino had been kidnapped before Morihiko Dan himself was. She's later found alive and rescued.
Elfen Lied: The random, forgettable Agent with sunglasses who was secretly working as a mole for the not-so-good guys of the Japanese government in order to steal information about their Diclonius propagation plot and hopefully a vaccine if possible, as well as cover up their own asses.
In Endride, Louise is a member of the Truculent and has been feeding information about the Ignauts to Delzaine for some time. Demetrio had actually figured it out, however, and relied on the character's Becoming the Mask to work to their advantage in the end.
Mest is actually a member of the Magic Council infiltrating Fairy Tail for the S-Class exams.
Subverted at the end of the Tartaros arc when Makarov reveals he was a member of Fairy Tail all along; he erased his own memories to make it easier to infiltrate the Magic Council.
Gajeel was shown conspiring with Raven Tail shortly after his supposed HeelFace Turn. Then it turns out that he's actually on Fairy Tail's side after all, and is only pretending to work with Raven Tail. Ivan is quite surprised to learn this when Laxus drops that little bombshell during the Grand Magic Games.
Avatar believes that the Magic Council has a one such mole among their number, with inner circle member Jerome in particular believing it's the newest big addition to their number: Gray Fullbuster having undergone an apparent FaceHeel Turn due to his Devil Slayer Magic overtaking him. As it turns out, he's half-right: there are actually two moles, with Levy being the spy for the Council masquerading as a rank-and-file cultist, while Gray is spying on them for his own separate agenda with Erza.
One bad guy's identity was hidden until chapter 71, where it was revealed that Selim Bradley, the cute son of the Fuhrer, was actually the biggest, meanest member of the Big Bad crew as Pride, the oldest homunculus. His adorable nature pre-reveal made it amazingly shocking, and his creepy nature since (especially upon being found out by Lt. Hawkeye) is quite the change.
Zanpano, who after joining the heroes, calls Envy to apparently tell him their location. Turns out the call was actually a trick to lead Envy into a trap.
In Gravion, Mizuki Tachibana, a seemingly normal (except her breasts) Ms. Fanservice, turns out to be a spy for The Federation, feeding information of the titular mecha to create their own (since they distrusted the good guys despite having the same goal of protecting Earth). She is rewarded with a life of luxury, but quickly grew miserable and bored with it, prompting her to return to the good guys. Overall, she sees her stint as a Necessary Evil, she thought that the only way for the Gran Knights to prevail is to have them work together with the government that distrusted them and had to let the latter catch up with the Gran Knights technology-wise to be of any help.
In the Hellsing manga and (eventually) OVA Walter C. Dorneaz betrays the Hellsing organization. This could be argued as a FaceHeel Turn but it is hinted as a long-plotted betrayal.
Innocent Venus. Jin. Turns out he hated his best buddy and former squadmate all along.
In Kill la Kill, turns out Satsuki Kiryuin had been planning to betray her Almighty Mom Ragyou since she was five, in revenge for her atrocious treatment of her little sister Ryuuko.
Original series Big Bad Dr. Hell had moles installed in several countries, usually infiltrated into centers of scientific research but also in army bases. The most infamous were Rico, an android Dr. Smith -a New Yorker scientist- had hired as his assistant and who later infiltrated the Photon Atomic Power Research Institute to sabotage the JetScrander, Erika, a female android who was supposed to infiltrate the Institute, but got amnesiac and befriended Kouji, and several androids impersonated different characters in order to wreak havoc (such like Professor Yumi, Dr. Smith or Kouji and Shiro's mother).
The Mykene Empire also had a mole infiltrated among Dr. Hell's henchmen, Archduke Gorgon, and Marquiss Janus tried to infiltrate into the Fortress of Science once by pretending being an average human girl.
Present Mic theorizes that there's one at UA High who's responsible for leaking a teachers' schedule and the location of the summer training camp to the League of Villains. Principal Nezu agrees, and one of the reasons the students are moved to on-campus dorms is to make it easier to smoke out the mole. Several arcs later, when All for One is informed that Izuku Midoriya has now arrived at the well-secured UA, he is still confident of the villain's victory as Touya 'has many friends'. One of those friends is none other than Toru Hagakure, revealed to have been the UA traitor the entire time.
After All Might retires, it's revealed that Hawks, the flying hero who rose up the ranks thanks to the shift in power, is a hero who is masquerading as a traitor to the Hero Association, working with the League of Villains to feed them information. In fact, the reverse mole is using his position just to find out more about the League's ultimate objective.
Being a series about ninja organizations, Naruto has several examples.
Medical ninja Kabuto is initially a mole in the Leaf Village for Orochimaru, and later a fake mole for the Akatsuki- pretending to inform to them on the Sound Village, but really remaining loyal to Orochimaru. Sai was initially a mole in Squad 7 for Danzo, but he switched loyalties almost as soon as he was found out. In one of the weirdest examples, Akatsuki leader Obito Uchiha is a mole within his own organization, as the HarmlessAnti-Villain Tobi.
Itachi. Too bad it was only revealed once he was dead. Even coming back as a zombie doesn't stop him from being loyal to Konoha.
His best friend Shisui was one as well, tasked by the clan to keep an eye on Itachi but instead sided with his best friend because he himself held the same devotion to Konoha as Itachi did. Ultimately he performed a Heroic Sacrifice, doing his suicide in such a way that Itachi would gain the Mangekyo Sharingan to aid him in the massacre.
Kaji from Neon Genesis Evangelion is secretly investigating NERV's inner workings and secrets on behalf of SEELE and the UN. He's also the mole in SEELE, feeding information and the embryonic Adam to Gendo Ikari behind SEELE's back.
Rob Lucci, Kaku, Kalifa and Blueno from One Piece. Yes, those are all from one story arc, and most are infiltrating one group. Specifically they were a government assassination group infiltrating the city of Water 7 (mostly its ship-building industry) to steal the blueprints for a Lost Superweapon.
Princess Vivi was a Mole in the criminal organization Baroque Works, trying to figure out the identity of its leader, who was planning to take over her country.
From the Punk Hazard arc, Monet and Vice-Admiral Vergo are moles in Caesar Clown's organization and the Marines, respectively. Both work undercover for Donquixote Doflamingo, so he can keep an eye on those two organizations.
The Zou arc plants the idea that there's a spy among the Straw Hat's allies. Years later in the Wano arc it's revealed to be Kanjuro, who is really related to the corrupt shogun and is actually really good at painting. The Mole was so committed to his role, he was willing to let himself be executed without ever revealing himself.
The referred shogun himself turns out to have one in his midst on the heroes' side, his top bodyguard, Kyoshiro, is actually Denjiro, one of the Nine Red Scabbards that prophecy says will rise to overthrow him. His appearance was warped by rage, allowing him to go unrecognized by ally and enemy alike.
One member of the Worst Generation is X Drake, a Navy Rear Admiral that defected and became a pirate. In truth, he's still working with the Navy as part of the task force SWORD, infiltrating Kaido's crew as an undercover agent. Koby is also part of that group. This info was so classified that prior to the Time Skip, he got caught up in a Buster Call on Sabaody Archipelago. Unfortunately, he ends up having to defend himself against his superior Admiral Kizaru, who had no clue about Drake's position. He survives said incident.
In Pokémon Adventures, it turns out that Sird was a mole sent by Team Galactic to infiltrate Team Rocket and learn more about space-themed Pokémon.
Meowth from the Pokémon Best Wishes anime pulls this off quite well. He pretends Team Rocket left him in order to let him steal their Pokemon. But when Pikachu finds this out, he goes ballistic.
Domino from Pokemon: Mewtwo Returns. One of her cover assignments was acting as a Pokémon Institute student under the teaching of Cullen Calix. When questioned about the veracity of her being part of the Pokémon Institute by Calix when she revealed her true colors, she confirmed she indeed was in the Pokémon Institute, and implied that Team Rocket has agents everywhere.
Deep Snow, the Northern General of the Imperial Army in Rave Master, was actually sent by Demon Card to spy in the Empire, and he later becomes the replacement for Shuda in Oración Seis.
In R.O.D the TV it is eventually revealed that Nenene's agent Lee Linho actually works for Dokusensha. This was a devastatingly effective deception, as he wasn't pretending to be a good guy; he was pretending to be completely uninvolved.
In Sekimatsu Occult Gakuin, Chihiro appears suspicious until it's revealed that she was helping Maya all along.
Soul Eater had a mole murder Buttataki Joe, and they made a bit of a whodunnit out of it. It's set up to make us think that Doctor Stein had done it, but several characters decided to have him investigate. He finds Justin Law, the youngest and most innocent-looking of the death scythes, is actually working for an Ax-Crazy human collector...and isn't that sane himself.
There's also Crona, whose actions under Medusa's orders were the cause of BJ being in Death City in the first place.
How far Justin was pretending to be a goodie is still up for debate. Though we know his background is more questionable than originally thought, one of the first claims about him was that he was highly resistant to the insanity wavelength in comparison to other humans. From what we've seen of madness in the cast, it wouldn't take much evidence to the contrary (recklessness, unnecessary violence, questionable motives/methods) for this clean bill of health to be thrown into question. Azusa might have found out he was tricking Shibusen all along, and alternatively she might have discovered reason to doubt his resistance. The fact he was sent to deliberately seek and annoy the Kishin probably didn't help, as it was presumably done under the belief that Justin was less susceptible than most to being affected by Asura.
The ladies of the cabaret club also count. Both witches, both seen to be very chatty with Death Scythe when he comes into drink/flirt/mope. As a result, they found out plenty of information about his work which they passed on to Arachnaphobia, though nothing (yet) that seems to have been terribly significant. The fact they'd managed it, however, was probably bad enough.
In Tenchi Muyo! GXP, The Mole is Erma. A double reveal, in that the identity of the mole is given at the beginning of the episode, but the reason why is only at the climax. Ryoko Balta is a shape-shifter. Erma was, in fact, an identity of hers. Since this is a Tenchi series, a Heel Face Turn and joining the harem happens quickly.
The higher ups already knew she was a Mole, but did nothing so they could secretly get information from her.
Sideways from Transformers Armada is something of a double mole. First, he's pretending to be a goodie, then 'reveals' that he's a baddie, spends some time messing with the other baddies' heads, then later reveals that he's a different sort of baddie.
The biggest surprise of Trigun was Wolfwood's identity as a mole, but he manages to turn this into a HeelFace Turn through Vash's influence.
Vampire Hunter D, in the 1985 film. While D is rescuing Dan from Rei Ginsei, Dr. Fehring takes Doris Lang to a safe location. When Dr. Fehring and Doris meet Count Magnus Lee's daughter Lamika, Dr. Fehring reveals that he was turned into a vampire the day before and turns Doris over to Lamika.
In Vinland Saga Gunir is a mole. One of the characters states he doesn't trust him before Gunir even has a chance to leak information, so it's not a huge surprise when it's revealed.
Zombie Land Saga:Itou was a government mole sent to suppress any potential Saga insurgents.