Monaca from Absolute Despair Girls: Danganronpa Another Episode at first glance seems to be a nice and cheerful girl. In reality, she's a manipulative psychopath, who deliberately triggers her friends' past traumas and plays mind games with people while maintaining a cutesy facade. It helps that she's the protege of series antagonist Junko Enoshima, who also falls into this herself and has similar dealings with her own followers.
April May's boss, Redd White, also qualifies. Mr. White passes himself off as a quirky and jolly, if egotistical, businessman. His penchant for unusual and sometimes wrongly used vocabulary is also played for laughs. Once Phoenix questions him too much though, his true colors are shown and he's revealed to be a vile blackmailer who enjoys lording his connections over his enemies.
A better example would be Morgan Fey, who acts like a supportive relative of Maya and a kind mother to Pearl. In reality, she's jealous of Maya's side of the family and sees Pearl as a tool in her Sibling Rivalry with Misty Fey.
And then there are the main antagonists of the third and fourth games, Dahlia Hawthorne and Kristoph Gavin respectively. Both polite and seeming like genuinely nice people; both are also sociopaths.
The killer of the first case, Frank Sawhit acts nice and friendly during his testimony. In Investigations 2, he acts like he's a fully reformed prisoner, but he's actually an accomplice to the real killer and he still has a habit of angrily throwing his toupee at those who question him too much.
Quecus Alba may look old, and he's considered a codophian hero. Later on, you discover that he was playing silly when he throws his façade; also, he tries to escape Miles's prosecution of him with his extraterritorial rights. Ultimately, he's the head of the allebahstian smuggling ring, and has killed four people note (two himself and two others with his mooks) .
Former Chief Prosecutor Blaise Debeste acts silly, cries crocodile tears upon seeing his juniors work hard, and jokes about "bullying" his fellow prosecutors, but he rivals Ga'ran as the most corrupt lawyer/prosecutor in the series by using his connections to cover up the assassination of the real President Huang, among other things. He's also not above intimidating and demeaning his son to prevent the latter from testifying against him.
From Dual Destinies also comes the phantom. He's one evil motherfucker, but, in Blackquill's words, he "cannot talk without another man's face", many of which aren't nearly as bad. Thus, both the affability and quirks of whoever he's impersonating and his own ruthlessness and sociopathy mix and come off like this.
Roger Retinz from "Phoenix Wright: Ace Attorney – Spirit of Justice" initially tries to suck up to Apollo and Athena because they're lawyers, but quickly changes his tune when he realizes that they're defending the person he's trying to frame. His stage personality, Mr. Reus, is polite and entertaining during cross-examination, but he's also willing to kill his biggest fan just to get revenge on the Gramarye family.
Queen Ga'ran Sigatar Khura'in from "Phoenix Wright: Ace Attorney – Spirit of Justice" tries to act like a reasonable ruler, a kind mother to Rayfa, and a Well-Intentioned Extremist who believes that executing defense lawyers when they lose is truly the best way to maintain law and order in her nation. The truth is that she only cares about making it harder for people to oppose her, especially the lawyer that she framed for killing her sister, the previous queen. She's also emotionally abusive to Rayfa when the latter is too distraught to perform a Divination Seance.
Alpha Protocol has Konstantin Brayko, a brutal Russian mob boss who is a rather sadistic and brutal individual, but ends up more entertaining than disgusting due to a strange obsession with the 80s and just how plain loopy he is.
"John Doe" pulls this in Batman: The Telltale Series as well. He's really nice and helpful to Bruce when they meet in Arkham Asylum, but even if you weren't familiar with The Joker you'd realize pretty quick it's all an act and that there's something seriously wrong and frightening about him. Him asking for Bruce to "owe him a favor", acting as if you've agreed no matter how you respond, and his Post Credits Scene imply he's going to pull some seriously evil stuff on Bruce as well:
The other villain in the series Big Bad Duumvirate, Relius Clover, also has shades of this in his interactions with the cast.
Castlevania: Aria of Sorrow has Graham Jones. He seems to be a polite character inside the titular castle, visiting as a missionary from a church. However, his niceness turns out to be a ruse. His true motives are revealed when Soma reaches the Clock Tower, where he grows more aware of Soma and his allies.
Danik from Dead Space 3 is a departure from the usual crazy, screaming psychopaths or undead alien horrors that are the usual enemies. He's still ruthless and remorseless, but he's soft-spoken and almost hilariously polite even in the worst of situations. For example, take his line after Isaac escapes from yet another attempt by Danik to have him killed: "Isaac? Is that you? You are unbelievably hard to kill. Are you aware of that?"
Reaver in Fable III is perhaps the best example for video games. As his voice actor stated in the third video diary:
"Reaver is not as much immoral as amoral; he has no morality whatsoever — he doesn't even have a concept of morality."
Hoyt Volker, who acts very friendly towards his men and enjoys a round of poker with them. He's also a ruthless slave trader who forces prisoners to run across a minefield, burns one of his men alive for disloyalty and generally kicks the dog at every opportunity he gets.
This seems to be a trait of the villains in the game. Vaas is simultaneously humorous and horrifying, acting very personable with his victims, joking and talking plainly with underlying menace just before committing some new atrocity. Buck, meanwhile is a highly intelligent, witty individual who never the less revels in the fact that he is a completely depraved sociopath, such as making jokes about how he's going to rape one of Jason's friends while speaking to him.
De Pleur is by far the most sadistic character in the game but has the demeanor of a busy-body dad, only letting his sanity slip when he's unable to answer his daughter's phone call. Pleur's sole position in Min's administration is to torture people and chop them up afterward.
Pagan Min on the other hand is almost like a second lap of Troy Baker's turn as The Joker, right down to the flamboyant suit and Laughing Mad radio calls. He is ridiculously casual and polite to his subjects and enemies, only to spout his anger off in furious yet hilarious rants or bursts of extreme violence, depending on his mood. When a human rights organization criticized his rule, he invited the lead doctor and her family over, then kidnapped her family and forced her to run his blood sport arena as a twisted joke. he also had her family killed and has her in his control on the fake promise that one day she'll get them back. His manner when dealing with the main protagonist is noticeably familial, no matter how violent the subject of the conversation may be. In fact, the only person he isn't faking his affability to is literally the one person who can stop him. And you discover only at the very end that it was very much intentional.
Final Fantasy VII's Professor Hojo is a Mad Scientist who turns out to be ultimately responsible for most of the bad things that happen in the story, including involevemt in Sephiroth's Start of Darkness, Cloud's Fake Memories, Aeris's abduction, the Clones' creation, and Sephiroth's summoning of Meteor (not to mention some boss battles and glossed-over physical and sexual abuse of Red XIII). But the whole time, his basic personality is comparatively normal by the standards of VII characters, if rude. He gets lots of witty lines, and is quite friendly (and popular?) when you meet him in Costa Del Sol which just enhances the creepiness of the stuff he does.
FFX's Seymour Guado invites the heroes to his mansion, lays out food for them before seeing them, proposes to the heroine, and acts generally mild-mannered and soft-spoken. But when the heroes prove to be detrimental to his plan to kill everyone in the world, he holds no qualms about unleashing the terrors of hell against them. Even when preparing to engage your party members, he manages to sound affable:
"Ah, of course. "Protect the summoner even at the cost of one's life." The Code of the Guardian. How admirable. Well, if you're offering your lives, I will have to take them."
Final Fantasy XV has Ardyn Izunia, a grandiloquent, bohemian Chancellor who manages to be an Obviously EvilCard-Carrying Villain and nothing but friendly. He tries to justify his most villainous actions as him trying to kick the plot to get it moving according to what already was preordained to happen, and whether he has any agency or is simply a pinball of fate is debatable. While his murders are of people who would have died soon anyway due to their own actions. His casual villainy seems to take a form closer to convoluted magic pranks, and seems to be an attempt to annoy Noct rather than inconvenience him. He spends the rest of the time making genuinely funny jokes, rescuing the heroes repeatedly, and at one point escorting them to their destination with bodyguards. Episode Prompto takes it into even a Trickster Mentor territory, implying that his reason for splitting the group up was in part to engineer a personal growth experience for Prompto. All of this though beguiles what an utter psychopath, Ardyn is and the sheer petty lengths he'll go to, so he can succeed.
The killer of the Five Nights at Freddy's series manages to be this without even speaking. Wherever he goes, he wears a smile, and death usually follows. A great example would be in the Foxy mini game in the second game. When Foxy comes out of Pirate Cove, he sees the killer smiling at him. The killer makes no attempt to harm Foxy, he just keeps smiling at him. When Foxy goes to see the children, he finds that the killer slaughtered them all.
Kid Icarus: Uprising's Hades loves making jokes and almost always has a smile on his face. However, it takes all of half a chapter from his introduction for him to reveal his cruel, calculating nature.
Kingdom Hearts: Master Xehanort and most of his incarnations are polite and eloquent, especially when they explain their evil plans. Despite that, they're all sociopaths who don't care how many worlds they have to ruin to gain the power and knowledge of Kingdom Hearts.
King Boo in Luigi's Mansion: Dark Moon talks to Luigi like he's having a friendly chat. He does this while explaining his plans to conquer the Mario world and has already proven to be perfectly willing to put the entire universe at risk if it means getting revenge.
The Illusive Man in Mass Effect is incredibly polite, classy, and cultured. Even when he gets pissed, he barely raises his voice at all. He does this just to make it very difficult for someone to tell whether he's lying or not. He drifts very clearly into this trope in the tie-in novels; while preparing a treacherous subordinate for a Fate Worse Than Death, he speaks in a regretful tone about how there is nothing personal in this, how much he enjoyed working with him, and how sorry he is that he must make this necessary sacrifice. What separates him from true Affably Evil in this exchange is that it is personal (he was furious when the man betrayed Cerberus), he deliberately puts the man through more pain than is strictly necessary for the experiment, and he acknowledges to himself later on in the book that he had allowed his desire to see the hideous retribution in person cloud his judgement.
Skull Face from Metal Gear Solid: Ground Zeroes is one of the most polite and well-spoken villains in the series. He is also quite possibly the most horrific, having done such things as having Paz tortured and gang-raped while forcing Chico to watch him do it. And then forced Chico to rape Paz himself.
Surprisingly, there's only one truly good example from the No More Heroes series. Destroyman adores causing pain and killing people, with a nasty Evil Laugh when he succeeds and a lot of Evil Gloating. Amazingly, he is really good at selling himself as a normal mailman. When he came back in the second game, however, one half of him was like his past self but more convincing...while the other half was Ax-Crazy, obviously angry but also really loving doing what he did.
Okage has Evil King Stanley Hihat Trinidad the XIV, a Living Shadow that spends most of the game attached to Ari. Despite being a Harmless Villain (most of the time), making it no secret that he intends to take over the world, he provides a majority of the hilarious dialogue found in the story. Mostly found in his interactions with fellow party member, the HeroRosalyn.
Yōko from Onmyōji who at first seems nice and polite enough to the heroes (hell, he even refers to himself as shōsei, a very humble and formal first-person pronoun) only to be later revealed as the one repeatedly abducting young yōkai girls.
Yōko:(to Koi-no-sei, a cute mermaid he's holding captive) It's come down to this and you still don't understand? Well, I'll have you know: you have been tricked.
RosenkreuzStilette: Iris Sepperin is very polite and sophisticated but she orchestrated the whole war and killed her own father and had Karl imprisoned for his attempt to kill her. Her fake friendly demeanor even allowed all of RKS to trust her without knowing she started the coup for kicks.
Persona 2: Tatsuzou Sudou from Eternal Punishment can be quite polite when situation calls for it and even shows some genuine respect towards the heroes in regards to their sense of purpose. This kindness however only runs skin deep and underneath it he is but a callous man, perfectly willing to back-stab his own followers or even doom the world just to advance his goals.
Persona 3: Shuji Ikutsuki. He's seems kind, he makes silly puns, he always answers your questions and generally aids in the mission to bring down the twelve Arcana Shadows. However, it turns out that he's just been using the protagonists to bring about The Fall, in addition to being fairly clearly insane. A cutscene in FES reveals that his jovial personality was indeed genuine, showing him making up puns in complete solitude where there would be no need to maintain a pretense but this is mean to enhance his creepiness and malevolence rather than lower it. Though his motives for bringing about the Fall seem more along the lines of Dark Messiah, rather than Omnicidal Maniac, that's simply because he wants to rule the world.
Persona 5 has Black Mask, real name Goro Akechi, who acts perfectly polite and civil to the whole world even while he's blackmailing the heroes, murdering innocent people, causing innocent people to murder others, and scheming to backstab and ruin the other villains. He's even polite until the final confrontation with him, at which point he inflicts a magically-induced Villainous Breakdown on himself and starts trying to brutally murder the Phantom Thieves.
Lovrina of Pokémon XD: Gale of Darkness projects a cutesy Valley Girl demeanor that belies a calculating, sadistic mindset that takes pride in torturing Pokémon and inflicting them with The Corruption. Best seen in her opening battle animation, which begins with her giving a cute wave with a winning smile that quickly morphs into a full-blown Psychotic Smirk.
GLaDOS of Portal, who continues to sound sarcastic and cheerful even as she tries to murder Chell.
Gla DOS: Burning people! He says what we're all thinking!
Father Donald Earl McArthur from Rides With Strangers is a Pedophile Priest who has killed, raped, and tortured many, and wants to purge the world of those he considers "heretics". He speaks to the young hitchhiker riding with him in a very polite manner, which only highlights his creepiness, all while planning to kill her if she says the wrong thing or nothing at all.
Charnel of Sacrifice, the amusingly bloodthirsty God of Death who also gets some great lines.
Charnel: "I am Charnel. God of Strife, God of Slaughter, God of DEATH! Where there is pain, I'm there. Where there is suffering, I flourish. Where there is joy...Yes, well, one could hardly have joy without another's suffering, no?"
The Boss may seem reasonable and even jovial at times, but if you cross him, he will not hesitate to end you utterly, no matter what the cost and regardless of how many lives are lost in the process - especially if you harm one of his lieutenants.
Otani Yoshitsugu from Sengoku Basara, in the English dub (the Japanese version is Obviously Evil), is constantly affable and polite (provided you haven't pushed his Berserk Button) even as his overt misanthropy and ambitions to spread misery to every human on Earth makes it clear it's all just an act.
Justified in Er's case, since she's the evil Split Personality of Vene, thus she knows the best way to sound appealing and friendly while tempting her other personality into giving up on world salvation.
At a fairly early juncture in Shin Megami Tensei, you encounter Ambassador Thorman, who is deeply concerned about JSDF leader Gotou's attempts to use demons to prevent the Americans' peace efforts and wants your aid. He's actually the Norse god Thor himself, acting on orders from the most holy YHVH Himself, and intends to drop his Mighty Hammer (that is, several ICBMs) on Tokyo to annihilate everything in it, including the JSDF, the demons, innocent civilians, american troops, and the heroes. Yes, even if you decide to take his side.
Vincent from Silent Hill 3, who tends to flip-flop around in this area: yes, he's a jerk, subtly insults you, and is a member of The Order. But he also doesn't want to resurrect The Order's God, and sends you off on a quest to acquire an item to supposedly beat said God. Why does he help you? Because if God were to be resurrected, he wouldn't be able to make any more money.
Walter Sullivan from Silent Hill 4 is this full force, the first time you meet him he's simply a soft-spoken man who sits on a flight of stairs and talks to you, leaving behind an item afterwards for you to take. You then find out that he's the serial killer who had chained you inside your apartment after he tries to kill your neighbor. Also, the item he gives you is useless and possesses your inventory box should you put it in there.
Despite being relatively calm and collected, Dr. Eggman Nega, Eggman's alternate-dimension counterpartnote or his descendant from 200 years in the future, pick your backstory in the Sonic Rush Series, is much more vicious than the Affably Evil doctor we all know and love.
Kerrigan becomes like this in Brood War. No longer just a bloodthirsty zealous slave to the Overmind, she develops a prepossessing, well-mannered, and regal demeanor to her guests and allies (that is, before she betrays them and lets them be devoured by the Swarm). At least, until she's de-infested at the end of StarCraft II: Wings of Liberty...and, thus far, even after her experience on Zerus, has not returned to her Queen Bitch of the Universe ways. Mengsk also qualifies, up until he gets completely obliterated by a vengeful Kerrigan.
One of the first missions for the Sith Inquisitor has them join a sith lord in torturing an acolyte for information. The sith lord in question would seem like an amiable personality were it not for the fact that he's instructing you in torture.
Lord Drowl is very excited to try out a poison called quell.
Arguably Lord Zash in the Sith Inquisitor story, but she may be genuinely nice (in her own opinion, anyway), depending on how you see her personality. True, she will try to hijack your body to extend her own life but it could be that she really just doesn't see a reason for you to object and thinks she's doing a favour for you as well, since, after all, you get to host her.
And of course player characters can exhibit this behaviour as well; it would seem that the Imperial Agent and Sith Inquisitor have the most conversation options to that end, though it also depends on the player's own interpretation of the character, naturally. It works with all classes, though: due to the nature of the dialogue system, you can threaten the lives of innocent children one moment and make polite conversation the next.
In Super Mario RPG, when Mario and his entourage finally meet Smithy, he at first seems far more polite and civil than most villains in the game. This is a facade, however, as he quickly proves just as nasty as the rest of the Smithy Gang, AND have an uncontrollable temper as well.
About half the cast of Team Fortress 2 are either this or normal Affably Evil. The Scout is just an asshole, The Spy is coldly professional, and The Sniper and Engineer are nice people when not being paid to kill, but the rest would probably do this for free, whether it's because death is just a normal side-effect of their hobbies (Demoman, Medic), they're crazy (Pyro, Soldier), or they just plain like killing (Heavy, Scout).
Tomb Raider (2013): Mathias feigns politeness and reason in his meetings with Lara and Sam, even managing to earn Sam's trust by bandaging her injured foot. In reality, he was bordering on sociopathic by the time of his first journal entry, in which he documents how he routinely tortures other people who wash up on Yamatai until they agree to join the Solarii, and kills those who don't agree.
In Ultima 7: The Black Gate, we have Batlin. A kindly sage and former druid, who is the head of the Fellowship and always working hard to help the people of Britannia. On the other hand, the Fellowship is a cult intended to subvert Britannia, spread distrust in the Virtues and Lord British, and pave the way for the Guardian to take everything over. In a hard-to-find dialogue (you have to cast the all-destroying Armageddon spell to get it) you find out that Batlin is driven by pure nihilism, having learned that (supposedly) nothing exists beyond death. (In the sequel, he is attempting to gain immortality for this reason.)
Professor Putricide from World of Warcraft is a funny, quirky old Mad Scientist who sewed his "children" together from a pile of corpses, and spends his time creating deadly plagues for the Scourge to use in their war against the living.
Handsome Jack in Borderlands 2, best shown in some points in the Southern Shelf. If you're doing the main quest, he banters with the player in a way that's not entirely friendly but seems more jokey than anything else (for example, he tells you that he was thinking of naming his diamond horse "Piss-for-Brains" in your honour). If you're doing a sidequest to collect some audio recordings of him, however, he puts on a seemingly apologetic pose when Helena Pierce tells him the cause of her scarring, then casually guns her down and laughs about the noise her head made when he shot her in the face.
In The Elder Scrolls series, this is a trait of Molag Bal, the Daedric Prince of Domination and Corruption, and quite possibly the closest thing to a true God of Evil in the ES universe. Molag Bal can actually act pleasant and polite, but he is not nice. At all. One of his favorite things is to corrupt a good and noble mortal, then seeing them snap, fall, or break. His methods include Cold-Blooded Torture, Manipulation, and even outright Mind Rape. He especially loves it when mortals do this to each other. One of Molag Bals most infamous acts (and that is really saying something) was to perpetrate the first rape, turning the innocent woman into the first vampire, who proceeded to rape and kill the nomads who cared for her and bringing undeath into Mundus (the mortal plane).