In Aladdin: The Series there's Mozenrath, Disney's most charmingly diabolical teenager. "Okay, then. Everybody else expires at dawn, while I blow away Agrabah. Then, say, noon-ish, I return and devise some way to destroy you."
Despite being insane, Barry from Archer is actually friendly and polite, at least until things go wrong. The cheerfulness doesn't even go away while he kills Jakov, which makes him even creepier.
Professor Tite-Gripp from Atomic Puppet acts calm, polite, and honourably, but as Joey and AP have learned the hard way, it doesn't mean he won't break his promises or outright lie if it benefits him and his evil schemes.
The villains on Batman: The Animated Series run the gamut, from genuinely Affably Evil as long as you don't make them angry to flat-out nasty and no fun at all to be around. The ones who most obviously fall into this trope are the Joker (of course) and the animated series' version of Poison Ivy, who here is one of the most ladylike terrorists and murderesses you can imagine - and is an outright Bitch in Sheep's Clothing as her everyday self, Pamela Isley. Making it all the more satisfying when the tables are turned on her and this smug beauty becomes a shrieking harpy.
Most of the villains in The Batman qualify as well. Special mention goes to this version's Joker, who is even more affable and even more murderous than his TAS counterpart.
Lawrence Lactavius Limburger from Biker Mice from Mars acts polite and sophisticated most of the time, but he's still a greedy bastard who shows absolutely no remorse whatsoever for the planets he devastated and the lives he ruined by stealing resources for his home planet Plutark and frequently attempts to kill the titular Biker Mice whenever they show up to thwart his schemes.
In The Boondocks we have Ed Wuncler I and his son Ed Wuncler II. Both of of them are ruthless businessmen and con artists who are very superficially charming, but show their true colors soon after duping people with their predatory business schemes.
Codename: Kids Next Door: The Delightful Children are freaky insane children who, despite being well-behaved around adults, are incredibly cruel to other children. However, they end up providing some of the most hilarious lines on the show, and they are fan favorites.
Katz from Courage the Cowardly Dog. A serial killer with a British accent. He always speaks politely even while trying to kill Courage. Really, his catchphrase "Ready for a little sport before dying dear boy?" says it all.
In Danny Phantom, Vlad Masters/Plasmius has a polite facade, but underneath is a monster wanting world conquest and to bang the hero's mom.
Mom from Futurama is a ruthless corporate raider and abusive parent who puts on a sweet old lady routine and fat suit for her TV ads. In her first appearance in "A Fishful of Anchovies", she drops the act when she finishes cutting a TV ad, and again when Fry gets in her way.
Calling Dipper "friend" while trying to cut out his tongue and kill him definitely qualifies Gideon Gleeful for this trope.
Bill Cipher zig-zags this trope. He'll talk to you in the most cheerful tone possible, while mocking you and ripping a deer's teeth out. Then he puts the teeth back. When the Pines twins foil him he will snap. HARD. When the group defeats him in combat... He'll compliment you and let you off easy. He easily and gleefullly sways between this and Affably Evil, by virtue of being certifiably insane:
Kuvira from Last Airbender's Sequel SeriesThe Legend of Korra is the quintessential Villain with Good Publicity and acts stern but infallibly polite in public, often to keep that good publicity. She even acts like A Mother to Her Men to her troops, telling them that she wouldn't put them through things she wouldn't go through herself. However, the facade only holds as long as things go her way or her subordinates do what she says. The moment something goes wrong or someone slights her, her temper disintegrates, the mask comes off, and out come the threats of a re-education camp. Bolin and Varrick learn this the hard way, as does her fiancé Baatar Jr.
Wile E. Coyote behaves like this when he goes after Bugs Bunny. A perfect example of this occurs in "Operation: Rabbit".
Wile E.: Allow me to introduce myself. My name is Wile E. Coyote, genius. I'm not selling anything nor am I working my way through college. So let's get down to cases: you are a rabbit, and I'm going to eat you for supper. Now, don't try to get away. I'm more muscular, more cunning, faster and larger than you are, and I'm a genius, while you could hardly pass the entrance examinations to kindergarten. (Bugs looks bored and yawns) So, I'll give you the customary two minutes to say your prayers.
Bugs: I'm sorry, mac, the lady of the house ain't home, and besides, we mailed you people a check last week. (goes down into his rabbit hole)
Wile E.: (returning to his den) Why do they always want to do it the hard way?
Season 2 villain Discord, in. He keeps up the act even while he mind rapes the Mane cast! The first time it slips — and the only time in the first part of a two-part episode — is when Fluttershy proves too accepting of her own faults for this to work on her and he gets furious. And the sudden snap just made it all the more frightening. He lets it slip again twice in the second part, first by taking obvious sadistic glee in finally breaking Twilight — mind you, this isn't just being happy he won; he'd already won by that point, and is just delighted to see his last opponent emotionally devastated and utterly crushed on top of it. Later it slips in favor of fear rather than malice when he realizes that all his plans thus far have failed and he's about to be defeated by the Elements of Harmony. Taken a step further in "Keep Calm and Flutter On" when he's assigned to live with Fluttershy until he can prove he's been reformed. He makes nice, despite continuing to wreak havoc with the laws of reality because he claims he's more comfortable that way, and eventually pretends he's actually had a Heel–Face Turn. All the while trying to scheme his way out of being eventually turned back to stone when he drops the guise. Ironically, he ends up Becoming the Mask and becomes her genuine friend. Keep in mind, however, he's still a major trickster, is generally unhelpful and seems to play nice while wreaking some havoc on the side. It's just that he generally isn't as malicious while doing so.
To a lesser extent, the minor antagonists Flim and Flam from later in the series fit this trope.
Sylvester Sneekly puts on the facade of a kind and caring guardian to the titular heroine. Even as The Hooded Claw he never loses his cool and remains calm and composed even as he explains to Penelope in great detail how his perils work, using terms around her such as "my dear sweet Penelope" only breaking the calm when his perils fail or to take out his anger on his henchmen, and even then his snarky tone remains. Even as Sneekly he gives off very subtle hints to Penelope that HE IS The Hooded Claw and she still doesn't get it because she's a Wide-Eyed Idealist and would never think her guardian would be such a horrible man.
In Reboot, Megabyte's sophisticated mannerisms and pretense of wanting to conquer Mainframe/the entire Net to establish order all hide his true predatory nature. The few times he drops the act, he's a snarling monster.
On the surface, Aku is a comedic, likeable villain, to the point of being able to have comic and civil conversations with other people, including his Arch-Enemy Jack. But, being Made of Evil, he is also a monstrous brute who loves to inflict as much pain as possible in other people.
The High Priestess from Season 5 as well. She's rather refined, classy and formal for a violent, Abusive Mom.
In Story for Steven, Marty acts as Greg's manager. He shows very friendly behavior towards Greg and Vidalia (whom he had presumably impregnated during that time), but the things he says reveal him as a greedy, posessive, abusive womanizer, causing Greg to kick him to the curb.
Greg: (cheerfully) He's dead to me.
In Drop Beat Dad, Marty returns, supposedly to spend some time with his and Vidalia's now-teenage son, Sour Cream. Marty helps Sour Cream set up a concert on the beach to "make up for lost bonding time", but suddenly reveals that the concert was only about a sponsorship with a (gross) soda-brand, and that he was using Sour Cream as a way to make him more money.
Roger may be the king of this trope, however; he has an extreme Lack of Empathy that shows an indifference for his family and friends' well being, and frequently commits all sorts of callous or outright murderous acts for minor indulgences or offenses, and so it goes without saying that he is a fan favorite.
This trope was also played perfectly with Steve's friend Barry turning out to be conniving, cunning and British; this is thus extended when he forces others to perform trivial things (such as play board games) at gunpoint. He is a completely different person with his meds. Two points go to Santa Clause in Christmas episodes. Still thinking of the Jolly Ol' Saint Nick when we hear that name? This version of the character is not so jolly, at all.
Carter Pewterschmidt, father of Lois. Proud to be an asshole, he uses his mass fortune to be a Jerkass to people - yes, that includes orphans. Yet, he's a fun guy and a kid at heart.
Let's not leave Peter Griffin out as well, he's a close second to Roger, with his mental disability as a poor excuse.
Prior to the mass Flanderization of the cast, Stewie was cast a psychotic mastermind vehement on taking over the world and killing anyone who gets in his way (particularly his mother), usually making for some of the show's earliest laugh-out-loud moments. Granted, as time passed in the show, Stewie's personality calmed and he gained redeeming aspects, ironically making him one of the few genuinely sympathetic characters in the show.
Slade in Teen Titans is softly-spoken and tries to present himself as a mentor and father figure to both Robin and Terra at various points. He's also cruel, manipulative, and brutal, and positively radiates creepiness.