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.
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.
To some degree, Seņor Senior, Sr. from Kim Possible 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."
To say nothing of Dr. Drakken.
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.
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 invites his employees to go golfing with him), who also just happens to want to take over the world, Bond-villain style. His Villain Song helps even further; apparently his twisted, twin obsessions are ruling the world and his employees' health! He also loves German beer.
The staff actually 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.
Mister Burns is sometimes this, depending on the episode.
Sideshow Bob also qualifies.
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.
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!
Gargoyles was very good about having layered and complex villains, particularly for a kids' show. David Xanatos, seems to like the gargoyles and doesn't really mind them always ruining his plans, either because he somehow wins anyway or because he considers Revenge "a sucker's game" anyway. Macbeth, while not as friendly, actually is closer to the gargoyles in terms of morality, though he's willing to go to extreme ends to achieve his goals.
Whenever a Megatron 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.
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. He is much quicker to Kick the Dog than most human antagonists throughout Transformers History, however.
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.
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.
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.
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 that turns out he secretly did a Heel-Face 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-Heel-Face 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 Heel-Face 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.
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.
On The Fairly Oddparents, Anti-Cosmo is a proper gentlemen who loves his wife, sips tea, and wants to generally make things hard for people. HP is also fairly polite, he just wants to force every living creature to be ultra orderly. Doug Dimmadome is also rather friendly if you're not getting in the way of his goals.
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. Also doubles as a Well-Intentioned Extremist who just wanted everyone to be happy.
It is implied 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.
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.
In Looney Tunes, 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.
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 3 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.
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.
Robot Devil in Futurama 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.
King K. Rool in the Donkey Kong Country cartoon. One episode where a movie was being made had him cast as the hero.
Satan is often portrayed this way in South Park. He's certainly less evil than Cartman.
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.
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.
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.
Lilo & Stitch: self-proclaimed Evil Genius Jumba Jookiba is a decent and sociable guy when not unleashing genetically engineered monsters to cause havoc and destruction.
Disney/Frozen: Both Hans and Duke Weselton are this. Both will kill to have their way (for Hans to get Arendelle's throne and for Weselton, to secure trade advantages) but show care and concern for their soldiers as well as the people of Arendelle.