Grandma Taters, an alien grandma who would just as happily knit Jimmy a hat or offer him fudge as turn him and the entire city of Retroville into cheerful, mindless meat puppets. She also doubles as a Well-Intentioned Extremist who just wants everyone to be happy. It is implied, though, that she eats brains, though. Even this is played affably, though, with others of her kind offering her "brain juice" to console her over her failure.
Adventure Time has Marceline, the Vampire Queen, who, despite possibly being evil, is so affable that she's one of the most popular characters on the show. She does use her mean side about as much as her nice side, but she's generally mean in a "bullying older sibling" kind of way.
In one episode Finn becomes Marceline's slave to help out her old slave, and she makes him do a number of scary things (which all turn out to have good reasons). Such evil things include raising an army of the dead (so that they can go to a party), and slaying a cute living plant (which turns out to be a man-eating monster). They become friends afterwards.
Her father, Hunson Abadeer, is incredibly friendly as well despite pretty much being the show's equivalent to Satan. It must run in the family. Though really he's a good mix of this and Faux Affably Evil, he can appear as friendly when he wants, but a lot of the times it's just to unnerve his victims to let their guards down or terrify them. Even around his own daughter all that pleasant talk he did was just to manipulate her into taking his place in the Nightosphere. He does love his daughter and can be genuinely nice at times, but it's more a ruse then not, and he loves her in a rather unhealthy way.
Though averted in the Official Adventure Time Encyclopaedia, which is written in-universe by Hunson, and written in real-life by his actor Martin Olsen. Every character profile (except for Marceline) is him talking about how disgusting and beneath him they all are and that they won't be spared when he conquers Ooo.
Archer: Most villains seem like this compared to the Jerkass parade that is the main cast.
Characters who turn out to be Evil All Along will still remain just as polite post-reveal as after. Rona Thorne, Conway Stern, and Charles and Rudy are good examples.
Iroh appears to be this in the first season. A mellow, easy-going, Cool Old Guy who loves tea, Pai Sho, and just relaxing. He also just happens to work for Zuko, his Troubled, but CuteAnti-Villain nephew (although Iroh is never seen doing anything particularly evil, and he never really helps Zuko make any major progress toward capturing the Avatar). But it turns out that he secretly did a HeelFace Turn several years ago and since then, he's never supported the Fire Nation in their quest to Take Over the World. And he's also a prominent figure of the Order of the White Lotus.
Pre-HeelFace Turn, though, he fit this trope to a T. In one flashback, he's seen writing a kind letter to his family in the Fire Nation while leading a brutal siege against Ba Sing Se (in the letter, he even casually jokes about the possibility of burning the city to the ground). Later during this siege, his son died, and this seems to have triggered his HeelFace Turn, possibly because of the uncomfortable realization that this is the kind of emotional trauma that he's been inflicting on Earth Kingdom families for years on end.
Evil Chancellor Long Feng is a perfectly reasonable man, willing to give his enemies multiple opportunities to surrender, and an excellent host. As long as you don't try and mess with his Government Conspiracy.
In the sequel series The Legend of Korra, Varrick perfectly represents this trope. He is normally very cheerful and helpful to our heroes, but when it benefits him financially, he won't hesitate to backstab them. He is arrested in the end for the attempted kidnapping of the president thanks to Bolin and Mako, but he still treats Team Avatar as if they were friends and is flabbergasted when he finds out they're mad at him for what he just finished doing.
Zaheer from Season 3 of Korra is very polite and civil, even towards his jailers. When confronted by Korra about why he attempted to kidnap her and his reasons for what he's doing, he is very polite to her and compliments her and her ideology. He may want complete societal collapse and he was just stalling Korra in the Spirit World to kidnap her, but Zaheer's still a complete gentleman. Of course, he still proves to be a very dangerous man, murdering The Earth Queen, holding the amateur airbenders hostage, and nearly killing Korra by forcing poison into her body. After a few years in jail, however, he ends up being the one who brings Korra out of her funk, since he clearly regrets the role he played in bringing Kuvira to power.
Ghazan of the Red Lotus also comes off as such and has a perfectly pleasant conversation with Bolin, much to Mako's dismay.
Bolin, will you stop making friends with the bad guys?
Batman: The Animated Series had Grant Walker from the episode Deep Freeze, who was a rather friendly and pleasant old man who had spent his life building theme parks and who's followers and henchmen all seemed to get along with. His plan, however, is to gain the same powers as Mr. Freeze (which he does) and freeze first Gotham and ultimately the entire world to drive the entire human race to extinction, save for his tiny select group of followers.
Harley Quinn is in crime just for fun and for her strange love toward The Joker; she even has her own episodes struggling for rehabilitation. Other versions in other media show a darker and more violent personality.
Wesker the Ventriloquist is another example, of course his problem is his Split Personality of the violent evil Scarface (his Ventriloquist's dummy).
A decent number of the villains in Beware the Batman are this. Special mention goes to Professor Pyg and Mr. Toad who in this series seem to be Well Intentioned Extremists claiming they want to protect the environment, they also show that they do care about one another and show a decent amount of respect for Batman as an adversary.
Despite appearing to kidnap you if you say his name, Candlejack is really a pleasant villain. He makes witty comments, thanks one of his victims for calling his name, and has a soft spot for pumpkin p Why, thank you.
The Crumpets has Uncle Hurry and Aunt Harried. While being a rich couple who deceptively make money off the namesake family and the public besides other bad things, they are polite and charismatic.
Viggo in Dragons: Race to the Edge. He's polite, thoughtful, rarely loses his temper (although he's had Not So Stoic moments) and sees the conflict as a Maces and Talons game (the local version of chess) between himself and his Worthy Opponent Hiccup. Lampshaded by the twins:
Ruffnut: You gotta love the way he talks. "Hiccup, I'm afraid our time together has come to an end. I must now kill you, if you have no objections."
Tuffnut: Yeah, like he's not going to have objections! And then he'll go "All of your dragonriders must also go, with my sincerest apologies."
King K. Rool in the Donkey Kong Country cartoon. One episode where a movie was being made had him cast as the hero.
The Urpneys of The Dreamstone, serving the monstrous Zordrak is enough to give them sympathy value, but the majority of them are pitiful slobs that have little interest in their evil duties and a lot of the time make nonchalent small talk to the heroes (in particular Spildit, who has problems recognising they are even bad guys). Even more conniving Elite Mooks such as Sgt Blob and Urpgor are this in spades.
On The Fairly Oddparents, Doug Dimmadome is rather friendly if you're not getting in the way of his goals.
Stewie is this in the post revival episodes, unlike his old character who was more Faux Affably Evil. While he was once a Token Evil Teammate, he has now become much nicer over the course of the series.
Doctor Doom has always been this, but his animated version in Fantastic Four cartoon is even better, having a polite conversation with the captive Sue Storm and sincerely apologizing for kidnapping her. He even laments destroying New York because he never got to see Cats.
The Robot Devil is actually, most of the time, rather polite as a character, despite being a robot Satan, and the depths to which Bender sinks at times leave even him appalled. He even included his own hands in his roulette wheel of choices when Fry asks for a better pair.
A number of more incidental monsters qualify as well. Special mention to the unnamed giant one-armed head, who is so affable, he asks nicely if you'll get in his mouth before eating you, and is even perfectly amenable, if very disappointed, to taking no for an answer (although he does get very irritated if you're rude enough to ignore him).
Zombie Soos, to the point where he stops mid-zombie-rampage to watch TV.
Zombie Soos: Second thought, gonna flip the script; can I eat your brains, Yay or nay? Seein' some Yay faces over here.
Death of The Four Horseman of the Apocalypse on The Hollow. When the kids imply Mira might be able to save his horse, he immediately offers them refreshments and a place to rest. The second it looks like it might be too late for Mira to do anything about his sick pet however, he goes right back to threatening them.
Shannon on Home Movies is a mild version of this trope. (He's not evil so much as he is just a bully, but the show is about eight year olds, so a bully is as close to evil as you're going to get.) In his first appearance, he schedules a fight with Brendon and gives him tips on how to warm up before the fight. Later in the episode, he lets Brendon think he won, just to help out Brendon's ego a little.
Several villains in Invader Zim are Affably Evil, most notably Mortos der Soulstealer. In between granting ruinous wishes, he recharges his malefic hellborne powers by petting puppies, eating snacks, and having fun.
Several villains from Jackie Chan Adventures could be called this, but the one that sticks out the most has to be the Wind Demon. Of all the sealed demon sorcerers, he was the most relaxed, well spoken, and generally polite. Where the other demons who were released immediately set to begin their rampages, often while berating Shendu for not getting to them sooner, Shendu wasn't even present for the Wind Demon's release, who instead engaged in small talk with Shendu's thugs, and then joined them for lunch while happily eating his prison slop, and generally seemed to be the most approachable of the group. When reality was rewritten so that the demons ruled the Earth, all he seemed to be doing was lounging on his throne, watching masked wrestlers fight while his champion's fanboy fanned him and watched. While it was implied that the battles were to the death, it seemed remarkably mild given the rest of the world's condition.
Tarakudo as well. Despite being the season 4 Big Bad, he seems genuinely polite and well-spoken towards even his enemies, and unlike the other main villains he's a Benevolent Boss who doesn't take out his frustrations on the Dark Hand even when they fail. Still evil, but not quite nasty enough for the "faux" part in "affably evil" - his affability, when it shows, is quite genuine and never exaggerated or faked.
Señor Senior, Sr. falls into this. He's a genteel, wealthy old man...who took up supervillainy as a hobby because his life had become boring. Unlike the archetypal example, he does use Death Traps, although this seems to be because he feels compelled to follow the traditions of villainy, rather than because he enjoys them. In one episode, Ron even comments that Senior's a "bad man. Good manners."
DNAmy is the sweetest, kindest, sociopathic geneticist you could ever hope to meet. She's not a bad person... she just wants to pervert nature and science to create life size abominations unto all things good. Or "Cuddle Buddies" as she likes to call them.
Wile E. Coyote, in his pursuits of Bugs Bunny, introduces himself formally, hands out a calling card, and gives Bugs the option to just give up. Arrogant? Perhaps, but he's certainly not impolite.
Sylvester, being a cat, wants nothing but to eat Tweety Pie and Speedy. Except, he's also a loving father to Sylvester Jr, has managed to save the lives of both Porky Pig AND Granny on more than one occasion, and has even proved that his fatherly instincts outweigh his cat instincts when he unexpectedly 'fathers' both a baby mouse (A Mouse Divided) and a baby bird (Father of the Bird).
Marvin the Martian embodies this trope. Rarely raised his voice and was very matter-of-fact about his motives to destroy the world.Chuck Jones wanted to make a new enemy for Bugs who was the exact opposite of Yosemite Sam: quiet, polite, but incredibly dangerous.
Elmer Fudd, outside his obsession to bwast that wabbit, is fairly mild mannered, and actually takes the role of The Everyman whenever not playing an antagonist. This evolved to the point that director Friz Freleng feared Elmer was so docile he made Bugs look like an abrasive 'bully' against him. (In fact, this is one of the reasons the far more aggressive Yosemite Sam was introduced.)
Witch Hazel is more dangerous than the usual Looney Tunes villain, but she bears her victims no malice, and is so ebullient that it's impossible to hate her.
Dr. Doofenshmirtz is a mad scientist who's at odds with P&F's secret-agent-platypus, Perry. Except that he spends half his time doing stuff like trying to make the perfect sweet-16 birthday party for his daughter or sharing chicken wings with Perry after he's captured him. He really is a nice guy; it's just that, well, he IS a mad scientist, after all.
There's also Norm the Giant Robotic Man, introduced in "Greece Lightning". He's fond of spouting random dialogue more appropriate to a married, white-collar suburbanite than a killer robot originally designed to attack platypi on sight. He was built this way because abovementioned Doofenshmirtz watched a documentary about the platypi, while trying to figure out their weaknesses. Said documentary stated that biggest natural enemy of the platypus is man, so he decided to build a giant robotic version of a middle-aged man to defeat Perry.
Mojo Jojo. He wants to take over the world and destroy the Girls, but he's very friendly and suave, and doesn't act hostile towards the Girls in his free time, that is, as long as they don't push his buttons, and some episodes guarantee that he might not be truly evil.
The original series finale reveals that he's very much like The Brain just above, wanting to take over the world so he can make it a better place.
Big Billy from the Gangreen Gang. He's got such a friendly and cheerful nature for a thug, and only causes trouble because of Ace's bossy attitude.
In "Catastrophe", the girls discover that the slime monster was only tearing Townsville apart because it was looking for its lost cat.
In "Super Zeroes", a monster begins destroying Townsville, and the girls start changing into their new hero identities. By the time they're done, night had fallen and the monster had suddenly lost interest in destroying the city. The next morning, the monster resumes his rampage, and the girls begin their journey to confront him. However, they all run into inconveniences that held up their arrival, and the monster eventually stops his path of destruction again at night (even checking his watch as time passes). Finally, when the girls actually confront him and prove ineffective against him, the monster explains that the reason he was destroying the city and drawing the girls out to fight him is because he was taking up a tradition back at his home island.
Lurkey from Rainbow Brite. Unlike murkey, Lurkey is not really evil at all, only helping Murkey with his evil plans because he is too childlike to no any better. Lurkey actually likes Rainbow Brite and colors. Despite being an enemy of Rainbow Land, Lurkey is very friendly to the other residents. During a mission to investigate a house, he spends most of his time playing with a hamster.
Daemon from ReBoot. When she was first mentioned, everyone expected her to be a huge snarling monster of a Virus, not the sweet, gentle, messiah-like figure she turned out to be (actually lampshaded by Mike the TV, the first Mainframer to meet Daemon face to face). It turns out she's out to wipe out every sprite on the net, but she still remains mostly sweet and nice throughout the whole thing.
Also Megabyte and Hexadecimal. Megabyte is suave and sophisticated, and treats his minions with respect. Hexadecimal can go from being genuinely nice to insane at the drop of a hat
They're siblings. And Megabyte is the one who tortured his sister into insanity.
Krombopulus Michael, to comically absurd extremes. He's an utterly ruthless hitman who will kill anyone, anywhere, kills because he enjoys killing, and uses the fact that he has no code of honor as advertisement. Yet he's also incredibly upbeat and friendly both on and off the job, making jokes and being polite as can be towards everyone he meets. Even when people attack or insult him, he barely reacts to it emotionally and keeps joking around like they're best friends.
"(cheerfully) Oh boy here I go killing again!"
Fart always speaks in a calm, soothing tone, and his stated desire for a cosmos without hatred is genuine. Too bad his idea of how to bring that about involves destroying all carbon-based life.
Unity is a Hive Mind out to take over the Universe and eliminate free will. She's also really, really nice about it, and at least one planet has been significantly improved by her taking over.
The show hilariously turned Emperor Palpatine of Star Wars into one of these. He's every bit as heinous as he was in the films... as he's chatting pleasantly with his barber, hanging out in his office with friends and laughing about the time he 'threw the whole senate' at Yoda, and joking about the force to the server in the Death Star's cafeteria.
Palpatine: (Seriously) I sense a disturbance in the force... (With a big grin) You didn't give us any crackers!
This is Bossk's main trait. He has his boots taken off before the briefing with Vader and berates the other bountyhunters for not doing the same and equips them while the other bountyhunters runs for their quarry.
Bossk: "Am I the only one polite enough to take off his boots?"
Scorpia, like Catra, is a Force Captain for the Horde, planning invasions and leading various missions and battles against the heroes. She's also incredibly friendly to pretty much everyone see meets, loves hugging her comrades, and just a sweet individual overall.
Entrapta is an energetic and curious person who just likes experimenting. The only reason she's even working for the Horde is because of her friendship with Catra and Scorpia, who were sympathetic to her when they all erroneously come to the conclusion that the Rebellion abandoned her in the Horde (the good guys actually thought she died). The lack of restrictions given for her research is also a bonus.
Hank Scorpio, a one-shot character from the episode "You Only Move Twice". A Benevolent Boss and all-around nice guy whom you'd be happy to work for (he calls all his employees friends and invites them to go golfing with him), who also just happens to want to take over the world, Bond-villain style. It isn't an act, he's not actively trying to "manipulate" people, he's really just that friendly - on the principle that a happy employee is a productive and loyal employee. And what's so wrong with that?
His Villain Song helps even further; apparently his twisted twin obsessions are his plot to rule the world and his employees' health! He also loves German beer. You get the feeling that were Scorpio to conquer the world, it would be more like more like a pleasant benevolent dictatorship anyway than, say, Hitler.
At the end of the episode, Homer reluctantly asks him if he should leave Scorpio's organization because his family is miserable in their new town (not even knowing Scorpio is a supervillain), even though Homer himself was proud of his work for the first time in his life: Scorpio actually agrees that Homer should leave because it's the right thing for his family.
The staff wanted to bring Scorpio back as the Big Bad of The Movie but changed their minds and instead made a new character voiced by the same actor.
Sideshow Bob qualifies at times.
In "Pokey Mom", Marge befriends a prison inmate who had previously robbed the Kwik-E-Mart and shot Apu. The episode ended with him having another Ax-Crazy episode, but he was generally very polite and was an excellent artist. You feel like he'd be a great guy after some intensive therapy.
Warden: Lady, I know he charmed you with some "please's" and "thank you's", but he wasn't so polite to the guy he shot.
Apu: Actually, he was. He waited with me 'till the ambulance came, then ran like a deer!
Satan is often portrayed this way in South Park. He's certainly less evil than Cartman. One episode even implies that, while he was once the rebellious evil fallen angel described in the bible, he's mellowed out considerably over the years and become more of a Manchild who's merely doing his job:
God: Jesus, what the hell happened to you? You got kicked out of here for being a headstrong rebel. And now you're a whiny little bitch.
Blue Diamond is one of the three (formerly four) rulers of the despotic Gem Homeworld which brutally enforces an oppressive hierarchy and plunders and hollows out planets with no regard for any organic life that might be living there, but she is one of the few homeworld gems that views humans as more than just vermin and bonds with Greg over their loss of their loved ones, then kidnaps him with with the intent of saving him from a superweapon that she doesn't know was rendered harmless. Later on when Steven is put on trial for his mother's crimes against Homeworld (though they believe him to actually be Rose Quartz shapeshifted) she says she wants to inflict a Fate Worse than Death on "Rose", she insists on a fair trial, unlike her cohort Yellow Diamond who wants it over quickly. She's also the first of the Diamonds to make a HeelFace Turn upon realizing how awful she's been to Pink, and makes up for it by helping Steven and Connie return to Earth.
Thundercats 2011 has Turncoat Thunderian General Grune, who maintained a genuine, abiding friendship with his fellow soldier Panthro while plotting long-term to become The Usurper of his king Claudus' throne. Presuming Panthro will go along with his scheme to defect to series Big Bad Mumm-Ra, Grune sincerely offers to rule together. He also enjoys the company of Claudus' son Tygra, training him in swordfighting as a boy.
Whenever a Megatron in The Transformers is played as more intelligent and less shouty, this trope usually follows.
The Transformers Animated incarnation of him is eerily calm in most situations, and the treatment of his troops is similarly so. Not once is he seen to abuse his loyal subordinates (The Starscream is another matter), and if he's annoyed with them, he doesn't raise his voice. Plus, how does he win over fresh recruits? He gives them rhetoric, over a chalice of his own special blend of oil.
Also from Transformers Animated is Sunstorm, the embodiment of Starscream's Sycophant nature. He's always going into battle with a smile on his face and a compliment: be it for Swindle's schemes, Sentinel Prime's ruthless tactics, or Prowl getting creative with Stasis Cuffs (he liked that one so much he used it against Prowl, defeating him and crediting him with the idea). He's also one of the smarter and effective of the clones.
From the same show, Silas is quite polite and friendly, in a brisk military sort of way. He even compliments his enemies on doing so well sometimes. However, it doesn't take long before he slides down to Faux Affably Evil, then becomes worse. The guy does not take defeats or setbacks well.
In VeggieTales, the French Peas often fall under this category, along with the Scallions.
Teen Titans Go!: almost all of the recurring villains are this. They regularly hang out with the heros, and one of them, Jinx is best friends with Raven and Starfire. Rose is also friends with Raven. Although they're most like Vitriolic Best Buds, because they beat each other up a lot too.
The Monarch's Henchmen #21 and #24 are two harmless, likable nerds who just happen to be Mooks for the Big Bad.
Arguably, most of the series' villains fits this trope. Due to the Guild of Calamitous Intent turning evil into a bureaucratic business surrounded by red tape. An example is that after Sergeant Hatred becomes the new arch villain, he sets up an appointment to see what Venture's allergic to, since it's part of the guild rules. He also says that, "There's no good reason on God's green earth that arching has to be a completely unpleasant experience for either of us." And he brought a gift basket with him. Though he's mostly being so nice to piss off the Monarch for stealing his technology.
In which case, Brock easily qualifies for this. While he's prone to go into homicidal rages and kill without a second's hesitation, he's also got a calm, collected nature and enjoys activities like gardening. He also provides good advice to the boys whenever they ask for it.
Essentially, all the villains can be described as a mild version of this, for while they're not "evil", they do tend to be mean, in a realistic way.
There are few villains in WordGirl who aren't this tropethe Butcher, Chuck The Evil Sandwich Making Guy, Dr. Twobrains, the Whammer Mr. Big, and Lady Redundant Woman all seem to have some degree of goodwill between themselves and Word Girl while simultaneously resenting her for thwarting their plans. When they aren't committing crimes, Word Girl admits that they're not bad people, and they enjoy pleasent conversations and small talk from time to time. Strangely, the only villians who don't fall into this trope are the ones who pretend that they're not evil at all, such as Granny Mae and Victoria Best.
In Xiaolin Showdown, despite Chase Young being an evil warlord who wants to conquer the world, he remains polite and cordial to the Xiaolin monks, particularly Omi and he always uphold his end of the deal if he loses the showdown. This is something that is even acknowledged by Omi when the latter points out that the good within him is stronger than he thinks.
In Young Justice, Black Manta uses an assassination mission to teach his son a lesson about honesty.
As is the robotic duplicate of T.O. Morrow. In his debut episode, he takes the defeat of his creation Mister Twister in stride, and even jokes to his assistant Brom that it was a good idea he convinced Brom not to pilot it himself.