Big Bad Dr. Hell from Mazinger Z 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.
And in Shin Mazinger Zero Dr. Hell created a mole believing she would work for him, but in reality she was a Reverse Mole, always on the heroes' side, and was only biding her time before defecting the first chance she got: Minerva-X.
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.
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.
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.
The biggest surprise of Trigun was Wolfwood's identity as a mole, but he manages to turn this into a Heel–Face Turn through Vash's influence.
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.
In the Hellsing manga and (eventually) OVA Walter C. Dorneaz betrays the Hellsing organization. This could be argued as a Face–Heel Turn but it is hinted as a long-plotted betrayal.
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.
In Fullmetal Alchemist, 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.
The Mole in Mahoromatic: Something More Beautiful is one the cast sees coming, but it doesn't do them much good. At least, she does a Heel–Face Turn when it counted.
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.
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.
Innocent Venus. Jin. Turns out he hated his best buddy and former squadmate all along.
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.
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.
Soul Eater had a mole murder Buttatake 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, 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.
Rob Lucci, Kaku, Kalifa and Blueno from One Piece. Yes, those are all from one story arc, and most are infiltrating one group.
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.
In Pokémon Special, it turns out that Sird was a mole sent by Team Galactic to infiltrate Team Rocket and learn more about space-themed Pokemon.
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.
Meowth from the Pokemon 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.
Nao from Bloody Cross. He appears to be an ally and talks about how much he hates villains, but it's all an act and he's actually a mole for Satsuki.
Becomes a source of Paranoia Fuel in Attack on Titan, thanks to the revelation that sentient Titans are in fact "humans in Titan flesh". 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.
In the Blue Exorcist manga, Mephisto reveals that there is a spy in the Esquire class... but nobody expected it to be Shima Renzou.
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 Fairy Tail, 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.
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.
In Brave10, Anastasia works for Hanzo and has been gathering intel the whole time.