In Attack on Titan, the Beast Titan politely asks Mike about his equipment and removes it without harming him. He then proceeds to tell the other Titans that they may have their way with him, since he's finished with his business.
Chang from Black Lagoon, who is openly friendly with the Lagoon Company. During his Breaking Speech moment with Rock, he reveals that his friendliness doesn't mean a thing.
Big Bad Aizen. Sure, he pretends to be a charming, laid-back guy, but in reality, he's just being condescending; other people are insignificant insects to him and he doesn't hesitate to tell them this, when he doesn't need them anymore. When he realizes Urahara's smarter than he is and Ichigo's a lot stronger than he is, the Mr. Nice Guy -act goes right out the window.
Tsukishima, in contrast to his Card-Carrying Villain partner, Ginjo. He acts polite and serene almost all the time, even while he Mind Rapes people with Fake Memories. When someone suffers a mental breakdown due to conflicting memories, the facade drops, revealing a sadistic monster.
Quilge is a sadistic Quincy commander who, in the Japanese version, talks in polite speech when addressing his opponents and talking about the bad things he plans to do.
Schneizel. He seems like a nice, charming man. Of course, he's a Britannian Prince, so not so much. He's introduced when authorizing the death of his sister's politically inconvenient, racial minority, Knight Of Honor, and proceeds to become the final villain, manipulating a mentally unstable genius into developing a nuclear weapon, then displays no particular concern as to how it is used, or who it kills, plans to destroy all the world capitals, and successfully destroys two Britannian cities. That's right. Britannian. As in, his own country. One of them was held by his self-declared enemy, and the other... well, just because his enemy was there.
Prince Clovis. Nice Guy, most of the time. Except when he's authorized illegal experimentation behind his father's back, and tries to kill a district of third class citizens to hide it. Not much screentime, though.
Genma from the second season of Darker Than Black is a pretty laid back guy who initially seems to be Plucky Comic Relief and keeps that attitude even after it becomes clear that he is a vicious psychopath. The first indication of his Faux Affably Evil nature is a train hijacking he does, wherein to create a distraction, he runs down tons of people and shouts out something like (paraphrased) "All aboard" with the mangled corpse of the actual conductor beside him. Also fitting this trope is the fact that while he's clearly a Depraved Bisexual pedophile, he expresses this through behavior and commentary that is disturbingly similar to your typical Lovable Sex Maniac.
Descendants of Darkness: Dr. Kazutaka Muraki poses as a polite doctor to cover up the fact that he rapes, tortures, kills, and experiments on children. He may seem charming at first, but that's hardly the truth.
Picodevimon from Digimon Adventure presents himself as a friend to several of the heroes and proceeds to utterly deceive them, all with an oily polite demeanor. He drops this facade when his plans go awry, though.
King Piccolo. He speaks politely to Goku and even praises his skills in their first fight after Goku lands a few blows and manages to knock him down... before beating Goku within an inch of his life. He also calmly offers one of the king's guards a position as one of his men. When he refused, Piccolo puts his hand through the guy's chest.
Frieza is fairly polite, when he's in a good mood... and an Omnicidal ManiacEvil Overlord, who will kill anyone who he feels is a threat to his power, in fear that someone will surpass him, going as far as driving entire species to extinction or blowing up planets just because he feels like it.
His father King Cold fits this trope even better. He calmly congratulates Trunks on destroying his son, offers to let him take his son's place, when told "no" asks to examine his sword... and then tries to kill him with it.
Perfect Cell is a rather good sport in battle and even gives his opponents sporting chances to beat him... Until he starts losing, then he becomes a sore loser who is willing to kill himself along with the planet out of spite.
Unlike Goku, Black Goku speaks in a soft, somewhat polite tone when addressing Future Trunks. His speaking pattern is actually quite formal. He also looks down on Saiyans, humans, or any mortal like they're filth, and sees death as a blessing to humanity. At the same time, he shows a great deal of respect towards Goku, who he calls the strongest of the proud warrior race. However, this sorta falls into faux too since he killed his version of Goku once he took his body.
The Caster/master pair in Fate/Zero usually act like normal people, even while shredding little children to bits with Combat Tentacles because they were bored. Caster himself enjoys pretending to be nice before horribly murdering someone for the extra shock value; his master seems to be just completely desensitized. Oddly enough, they also have the best relationship of all the master/servant pairings, despite the master having no magic. The good relationship is justified in-universe: When a master summons a servant without a catalyst (for example Kiritsugu used Avalon to summon Saber), the grail picks the Heroic Spirit who's personality is most similar to the master's.
Envy can sometimes be fairly amusing and seem like a Friendly Enemy, but it's all an act, and Envy is by far one of the most cruel and sadistic characters in the series. Father also might qualify. He can seem polite and reasonable and is even kind of goofy in his first meeting with the Elric brothers, but beneath it all, he's devoid of empathy and sees himself as so far above humans that he literally feels nothing, not even hate or contempt, towards them.
Solf J.Kimblee most certainly qualifies, too. He's shown many shades of Wicked Cultured and can be polite, charming, and an all-around charismatic fellow...when he's not making bombs out of women, children, and any other poor saps within arm's length.
Fuhrer King Bradley comes off at first as a charming family man and Reasonable Authority Figure. He's actually a ruthless homunculus, Wrath, who ordered the war in Ishval. Even worse in the 2003 Anime where he is revealed to be Pride, where he ordered that war gleefully, and remorselessly killed his own son
Gauron from Full Metal Panic! has a very quirky, highly amusing personality - while going around rampaging and killing people. Including his employers and co-workers. He has no redeeming qualities and has almost every vice and evil you can think of (being an Ax-Crazy, pedophilic rapist and necrophiliac that will kill anyone and everyone, just because, and gets jealous of and tries to kill a 16-year-old girl just because she's the girl Sousuke likes). But let's face it - it is very amusing to watch him mass murder while he cracks horrible jokes and acts all happy.
In the Girls und Panzer spinoff, "Little Army 2," Kilimanjaro, head of West Kureouji Grona, a school that copies St. Gloriana, is this. Like Darjeeling, she uses formal speech on her opponents, but does so in a highly condescending manner, particularly when showing up to taunt her school's longstanding rival Bellwall. It's perhaps exemplified, when, after hearing her little sister Nagisa tell her that she refuses to continue spying on Bellwall, in spite of being threatened with being forced out of tankery, Kilimanjaro smiles and slaps Nagisa across the face.
Muruta Azrael. His charismatic nature and excitable personality lead to a lot of morbidly funny scenes (and who can forget the infamous 'YATTA!' scene), but he's also a genocidalsociopath bent on wiping out every Coordinator that exists.
InuYasha: Naraku speaks politely, but it's obvious that it's merely a sign of mockery, somewhat justified as his current disguise was a noble who used royal dialect. After Mount Hakurei, he drops the act completely in favor of being a Smug Super.
From earlier on, there's Kaguro. He styles himself as a Magnificent Bastard and is conversational with Yoshimori when they fight. He's more towards the Ax-Crazy end of the Blood Knight spectrum. And he murdered Gen and is only an ayakashi because he was so completely insane as a human.
Nui Harime from Kill la Kill acts like she a particularly saccharine schoolgirl, keeps complementing people, and flirts with all the pretty girls around her. And yet, she is a huge bitch, and revels in it. Probably the most telling instance of this is Nui's reaction to when The Hero, Ryuko, tries to start a fight her without even activating her battle transformation:
"But enough about me! Show me your Godrobe! Are you holding back because I'm dressed like this? Didn't you see what short work I made of that Goku Uniform back there? You shouldn't hold back with that Godrobe of yours. Still not convinced? Well, I'll show you something neat. Here we go! Ta-dah! Yup, it's the other half of your Sword Scissor! Fresh off your father's corpse!"
Dr. Hell from Mazinger Z has a good helping of It's All About Me, but always keeps an educated, polite behavior and mannerisms, even when he is going to dissect someone to turn him or her into his next enslaved Cyborg.
Johan, the title character of Monster, has this as his specialty. He charms, he smiles, he seems to care and he's such a beautiful and brilliant young man... as he uses you and kills you and if he takes enough of an interest in you, he will probably take the time to kill all your hopes and dreams, first.
Michio, the protagonist of MW, really has a friendly personality, but is really a criminal who commits atrocious crimes for fun.
Gargoyle from Nadia: The Secret of Blue Water. He's willing to kill anyone so that his plans could go accordingly, yet he is so polite and refined towards his foes. Especially with Nemo and Nadia (who he calls Princess).
Deidara. Just as loud as Hidan and more flamboyant, yet he is stated by Pain to have joined Akatsuki only for shits and giggles. In fact, Deidara was forced to join Akatsuki after losing a bet against Itachi. It doesn't make him any less of an example of this trope, however - while really desperately trying to pass off as a "cool" villain he has to put up a humongous effort to hide his rampant insanity. That is, until the very end.
Gengo in Shikamaru's Story. He's initially appears Affably Evil and charismatic enough to convert anyone who hears him talk and get them to join his attempts to build a Shinobi empire. The first cracks in the facade show when So and Roku, Shikamaru's teammates from the Anbu, despite appearing to have bought into his ideology, appear to have been tortured. Once it's revealed that Gengo has been relying on a Compelling Voice to brainwash people to his side, and Shikamaru faces him in combat, Gengo loses his affability entirely.
Gengo: I will kill you, you bastard. And I will pull all those in the hall together into the same mind, and we will proceed with my ambition.
Arlong keeps a calm tone even as he slaughters humans out of sheer racist superiority, calmly lying to Nami for 8 years that if she gets enough money he'll let her go, then hires a corrupt marine to steal all the treasure she gathered just as she reached her goal, and calmly telling her to just start over as he just laughs at her! This is especially pronounced in the 4kids dub, when he cheerfully offers Luffy good conditions if he agrees to become a slave, and this line, after he sends Bellemere to the dungeon.
4kids Arlong: If you can't pay the cash, then you're out with the trash... and feel free to quote me! YEAH!
Crocodile seems like a calm and reasonable enough guy, but the second he gets (or fails to get) what he wants or finds out you've failed him in ANY way he drops the politeness and orders your death in the same calm tone.
Blackbeard is this and a bit genuinely Affably Evil. He might at first come off as a friendly sort of guy with a big smile on his face, but could quickly turn to killing and mocking you, all while wearing the same exact smile. Though for all his unpleasantness he does seem to genuinely care about his crew, despite gaming all of his newer members by making them fight to the death and taking the survivors. Granted they were among the most evil and unrepentant criminals in all of Impel Down but still. Plus his friendly demeanor whenever it shows for the most part IS genuine, which makes him all the more evil.
Caesar Clown is even worse, He managed to successfully manipulate various prisoners and Brownbeard's Crew into becoming his underlings by coming off as a great scientific hero to them "curing" them of their afflictions (with Help from Trafalgar Law) when in fact He's the one who poisoned them.The guy also came off as a kind caring "Master" to many children who ended up on Punk Hazard for his treatment of their diseases, when in reality he's been lying to their faces, they were kidnapped to be his Guinea Pigs, he's been drugging them for well over a year with his Fantastic Drug candy turning them into giants, worst part is that many of them might not live for 5 more years because of all the drugs they've ingested Caesar has done all of this without so much as breaking his polite facade even once around them, he's basically a mix of Frieza and The Joker. Funny enough he's played by Ryusei Nakao.
Joker from Smile Pretty Cure! acts like a fun guy, is almost always smiling, and speaks to Pretty Cure as if they're just having casual conversation...while he drives them to soul-crushing despair and laughs how they'll never defeat the Bad End Kingdom or revive the queen.
Keith White of Project ARMS has shades of this. He is very calm and polite towards the protagonists, before trying to kill them in the most violent, horrific way possible. In a flashback, it's shown that he spoke kindly to Alice when she asked him for a special present for her birthday and, upon hearing her request was to go outside with the other experimental children, he calmly hit her.
Ranma ˝: Nabiki Tendo is generally pleasant and easy to get along with, but she doesn't even try to hide her true colors: a completely amoral, ruthless, and greedy bitch with a complete Lack of Empathy and a Money Fetish that almost makes Mr. Krabs look tame by comparison.
Rosario + Vampire gives us Hokuto Kaneshiro. He makes friends with Tsukune, supports peace at Yokai Academy, is a strong, determined leader, and has a close friend... in the form of dancing-mad Kiriya Yoshi, and only because Kiriya is the one who gave him monstrel blood so he could fend for himself. Go on, Tsukune. Look away for a moment. You'll find everyone beaten to the ground, and Hokuto standing there with a stick in his hand, insisting that emotions are pointless. Oh, and don't expect him to be any better a year after you and Moka kick his ass - sure, he might have helped you stop his own plan, but he's still going to strangle you with his inconsistently-changing monstrel hand, gloating that you can't protect your girlfriend. Ouch.
Sugou from the ALO arc. He talks to both Kirito and Asuna as if they're friends, but both of them, as well as readers know right off the bat of just what an asshole he is. He threw it away sometime after.
Morte from Progressive. He uses polite speech and is fond of joking around and making bad puns, but Kirito's wary of him because of this, and for good reason. Morte threatens to alert the nearby enemies to Kirito's presence, thereby sabotaging his attempt at completing the quest, and it's soon revealed that he's been playing the DKB and ALS against each other for some unknown purpose. Kirito even notices this, along with acknowledging coming off as rude in comparison.
Morte: (after accepting a duel, during which he plans to kill Kirito), Roger that, man. I'm getting so nervous thinking about a duel with the Kirito. Can we take a photo to commemorate after the fight? Oh, wait, we haven't gotten to the point where screenshot items show up yet. Aww, too bad...
Eto pretty much embodies this trope. She frequently puts on a sweet demeanor, chatting with people in a cheerful fashion and offering them advice about their problems..... but is utterly twisted by her hatred of the world and takes pleasure in destroying the lives of others. In particular, she seems to enjoy a nice game of Corrupt the Cutie or Cold-Blooded Torture, often taking special care to destroy families in the process.
Dr. Akihiro Kanou has cultivated a kind and paternal bedside manner, always speaking politely to people. He's a prolific Mad Scientist that believes he is Above Good and Evil, utterly lacking in compassion and willing to use or kill anyone for the sake of his experiments.
Legato Bluesummers does a bit of this, although he is as freaky-evil as possible in his first meeting with Vash, specifically.
The anime version of Knives does a bit of this whenever interacting with Vash. Notably, his cheerful "yo, Vash!" upon their reunion in July, while sitting on a desk next to the just-murdered corpse of its owner, whom Vash was coming to visit. A similar but more elegant friendly greeting appears when Vash arrives for the final battle. However, because this demeanor only applies to his brother, and because he would probably not do anything to said brother if Vash just got out of his way, this may be more of a single-target Affably Evil.
Yami Marik would also count. In the original Japanese more so.
Dennis is like this in Yu-Gi-Oh! ARC-V; his polite and soft-spoken personality remains even after being revealed as a member of Duel Academy, but he's clearly as sadistic as any other member, vowing to destroy Shay slowly before his second Duel with him began, eventually dropping the act entirely when he calls it a "Hunting Game".
Muska from the Studio Ghibli movie Castle in the Sky fits this trope to a T. He pretends to be an affable, trustworthy man in service of the government, until he reveals he intended to use Laputa as his personal battle ship to dominate the world. He turns downright scary when the protagonists appear to foil his plot.