Cinderella: Lady Tremaine. She doesn't often raise her voice and can seem quite pleasant, but she loves the use of Exact Words, is a Manipulative Bastard when it comes to setting her daughters on Cinderella.
Maleficent of Sleeping Beauty is a horned fairy with pale green skin - and acts and talks just like the prim high-society lady she bitterly wishes she were treated as. Her worst moment is in Prince Philip's dungeon cell, where she "comforts" him by promising to let him out in 100 years to free Princess Aurora...at which point both he and his horse will be so old and frail they will barely be able to walk.
Shere Khan has a mock gentleman personality, speaking politely with Kaa while not so subtly threatening him. When he meets Mowgli, he mockingly gives him a 10 second head start because "that makes the chase more interesting... for me."
Kaa himself, who promises to protect Mowgli just as he's preparing to crush the boy to death. This goes for Scarlett Johansson's portrayal as well.
The Sheriff of Nottingham in Robin Hood is quite cheerful and polite on the surface, but it's just to toy with people. He'll take from the church's poor box, a blind beggar's cup, or a crying child's birthday present, and he'll enjoy every rotten moment of it—all the while asserting in his folksy Southern accent that Prince John sends his best regards.
The Great Mouse Detective: Ratigan. This is ultimately one of the things, as mentioned above, that makes his Villainous Breakdown all the more terrifying; he puts up a slick and suave exterior, but we occasionally see hints of his feral nature kept just under control...until the final showdown.
Ratigan: My dear Bartholomew... I'm afraid that you've gone and upset me.
Jafar from Aladdin is closer to this than to the Affably Evil he's sometimes listed as. Affably Evil might kill you, but it couldn't hurt to sing about humiliating you and make your girlfriend watch, right?
The Lion King: Scar acts like a kindly uncle towards Simba while secretly plotting his and Mufasa's deaths.
Shan-Yu from Mulan, depending on how you take his mild tone of voice. When the Huns catch two Imperial scouts, he kneels down and adjusts one of their scarves and compliments them for finding the Hun Army. He even lets them go, to tell the Emperor he's coming. And then has one of them shot In the Back. Also when he says that they should go through the village to 'return' a doll to a little girl.
Shan Yu: Go! Tell your Emperor to send his strongest armies. I'm ready. [The two soldiers scurry off, one after the other.] Shan Yu: How many men does it take to deliver a message? Hun Archer: One.
The Hunchback of Notre Dame has Claude Frollo, who affects a caring demeanor towards Quasimodo, acting as though his exile in the belltower is a kindness, saving him from the cruelties of the outside world.
Hercules has Hades as its Faux Affably Evil Big Bad. He talks like a used car salesman and makes wisecracks while screwing over everyone as much as possible. That being said, outside of his source material, he acts more Affably Evil instead in comparison to the other Disney villains, particularly in Mickey's House of Mouse.
Hades: Baboom. Name is Hades, lord of the dead. Hi, howya doin'?
Yzma from The Emperor's New Groove. Inverted when, after some of her henchmen are turned into animals, she calmly excuses one of them when he requests permission to leave and even asks if any of the others wish to depart.
Tangled: Mother Gothel's domineering mother act and her general manipulative personality is this in spades.
Wreck-It Ralph: King Candy. Oh, King Candy. At first glance, this little Mad Hatter knockoff seems about as harmful as a cube of taffy. But it becomes slowly clear that he's infinitely more malicious than he lets on. It also helps that he's an excellent liar, and savvy enough to have everyone, up to and including the audience, eating out of his palm.
Frozen: Prince Hans, as part of his status as The Sociopath. Again, he's good enough to fool the audience.
Zootopia: Bellwether puts on a facade of friendliness as a politician and tries to win Judy Hoops over to her side. When Judy refuses to join the anti-predator conspiracy, Bellwether wastes no time trying to engineer her murder by turning Nick savage.
Moana: Tamatoa the crab monster. He acts goofy and happily starts singing a very upbeat Glam RockVillain Song to Moana, then tries to eat her in the middle of it before delivering a savage beating to Maui.
Bradley Uppercrust III from An Extremely Goofy Movie. He's polite to team prospects (though passive-aggressive to non-prospects and others) but never means any of it. He's ruthless enough to deliberately endanger his opponents and leave his own right hand man to die.
Lord Shen, from Kung Fu Panda 2, is very pleasant and polite to his enemies, but he doesn't even really attempt to fool anyone that he is a violent monster. When his foes don't heed any of his warnings, he stops the threatening formalities and quickly proceeds to blow anyone up who opposes him.
Lord Business, the main antagonist in The LEGO Movie, is a practical embodiment of this trope. It is truly creepy how he can be completely conversational one minute, before descending into pure twisted evil without having to change his mood due to his sheer enjoyment of people's suffering. Of course, seeing as there's always something behind that expression, you can't trust this guy at all as anything he says is either dripping with sick joy at his manipulation of others or crushing wrath if you ever disappoint him. So plenty of treading on an incredibly fine line around him. Just because he's a LEGO figure... The scene involving Good Cop Bad Cop's parents and the inevitable erasure of Good Cop is full-blooded evidence of Lord Business' basis in this trope. Just watch his expressions and behaviour - you will not be able to argue differently.
Scarlet Overkill in Minions initially seems to be Affably Evil like most of the other super villains, but after Bob becomes King of England, she quickly drops the act and shows just how affable she really is.
Hopper from A Bug's Life has moments when he acts polite while or after doing something horrendous. While preparing to feed Dot to Thumper, he politely asks her if she's afraid of grasshoppers. After three of his gang ask why they have to go back to Ant Island, he behaves as though he agrees with them - that it would be a better idea to stay home; then he kills them, explaining that they're not returning primarily for food, but to keep the ants in line.
"Does anybody else wanna stay?"
Jackson Storm from Cars 3 is open and superficially friendly, but always has a couple of harsh barbs at hand.
Corpse Bride: Barkis attempts to make himself presentable and tries to put on a charmingly polite demeanor in order to wed Victoria. Even though it's clear to viewers that his intentions are no good.
The Other Mother from Coraline acts under the facade of a doting, loving, fun parent as a means of luring unsuspecting children. She recreates the Pink Palace and improves them, creating denizens and wonders that makes her world seem more appealing for the children before she traps them by sewing buttons into their eyes, holding their souls hostage. When Coraline rebels, she developed a Glamour Failure, her appearance becoming more exaggerated and monstrous as the film goes on and doing more twisted and inhumane things, all while behaving as if nothing has changed.
Archibald Penelope Snatcher from The Boxtrolls, both in his regular identity and as Madame Frou-Frou, acts as a productive member of society, gaining the support of the general populous for committing a "public service" (getting rid of boxtrolls) and entertaining them as Frou-Frou (which is really just anti-boxtroll propaganda to keep the public on his side). He maintains an air of culture and sophistication due to his ambitions of becoming an aristocrat, when really he is just a sociopathic thug.
When Kubo meets his grandfather the Moon King from Kubo and the Two Strings, he comes to Kubo through a dream, acting as a kind old man who leads him to his father's helmet when really he is leading him to a trap where the remaining Sister is waiting for them. When they meet face to face, the Moon King tries to talk Kubo into giving up his remaining eye and living with him in the Heavens. As their conversation goes on, the Moon King's mood shifts between jubilation of his own magnificence to disgust at the mortal realm and anger toward Kubo's defiance, signs of madness evident in the way he hunches and cackles as he does. After a while, he takes Kubo's defiance as a definite and drops all pretense, transforming into a monster with intentions of torturing and killing him to teach him a lesson.
The Sisters can count as this as well, laughing as they float toward him, asking him to "come to [his] aunties" so that they can take his other eye.
Nigel, the sadistic Dragon-in-Chief in Rio. He rarely outright insults someone, and tends to talk in a calm, friendly manner...while relishing in his villainy and "convincing" someone to be his Mook by dropping them from several hundred feet.
The Grand Duke Of Owls in Rock-A-Doodle. As a grand duke, he tries to act sophisticated, but his Hair-Trigger Temper ruins it. Even when calm it's clear his politeness is a façade.
"Hello, kitty? It's the duke. I'm afraid I have some bad news, I'm afraid. Ahem, when the batteries expire, so will your friends. And too-da-loo, cheerio, bye".
Rothbart from The Swan Princess: He killed the king and kidnapped the titular princess in order to gain control of the kingdom—because he learned the first time around that stealing it was not the way to go, and constantly remains one step ahead of the heroes. If not for blind luck, the main characters would be dead. He's also a Deadpan Snarker of sorts and never loses his temper.