24: Jonas Hodges. Charming, witty, charismatic, psychotic. When he suspects the chairman of the board of his company of helping the government in taking down his company, he engages him in a conversation discussing their long history together and the virtues of loyalty before savagely beating him to death with a glass pitcher. He then proceeds to dab the blood of the man he had treated like a son from his shirt with a wet napkin. That's just the most extreme example.
Agent Carter's Dr Ivenchko hypnotises an SSR agent into killing himself, but gives him commands to have a drink at his favourite bar first. There's no reason for this, except it's better for the guy to be happy and relaxed when he dies than otherwise.
Alias: Julian Sark is usually polite and almost never raises his voice. He even says "please" and "thank you" during very tense situations.
Holland Manners: charming, charismatic, and fatherly, particularly towards Lindsey McDonald.
Most of the people at Wolfram and Hart. They're all demons, vampires, murderers, and worshipers of Eldritch Abominations but otherwise they act like normal white-collar professionals in an office environment. For example, Izzerial from the Circle of the Black Thorn at Wolfram & Hart, comes across as an upwardly-mobile professional involved with networking. Listen to the character without looking at him, and, aside from the occasional reference to death, you'd be pushed to guess he's a demon.
Sahjhan. He's rarely without a one-liner, and chats up Connor, seemingly without malice, whom Sahjhan knows is destined to kill him in the fight that's about to start.
In a stunning Face-Heel Turn, the demon, Skip. Known previously for his gregarious nature, when Angel asks whether the character's a patsy or in on the latest evil goings-on, he smiles, shrugs, and says he's no patsy just before laying in to Angel. This, in turn, foreshadows the next Face-Heel Turn... Cordelia.
Angel: So, I'm thinking either you've been played for a dupe like the rest of us... or you've been in on this from the start, Skippy.
Skip: Angel, buddy, whatever's going on, I'm telling you true... [dagger shoots out of arm]Not a dupe.
Jasmine could easily be seen as this, although whether or not she's evil is debatable.
Holtz also qualifies as this to a lesser extent, being quite polite to the team and respecting them despite the fact they're on opposite sides.
Holtz also has no interest in killing anyone other than Angel (and Darla); he's perfectly nice to everyone else.
Bester tries to be this, and although he manages to be a character of great pathos and complexity, he's still a bit of a subversion — his efforts at affability are a creepily obvious front for a somewhat sociopathic and thoroughly broken personality.
Mr. Morden. Like Bester, he's a very broken individual, but in completely different ways. His veneer does crack when he's pushed too far, but there's only a handful of cases of that throughout the series.
William Edgars is a more genuine example. He's a Well-Intentioned Extremist who only takes the steps he does because he believes they're absolutely necessary. He's friendly to his allies and potential allies (and many others as well), and does what he can to minimize the suffering of his test subjects. If the measures he advocated weren't so extreme, he'd be a clear Anti-Villain (and even so, he manages to border on that trope).
Sheridan's torturer in season 4 is a middle-aged accountant who just happened to be delivering large electrical shocks and doses of agonizing, vomit-inducing poison, instead of doing tax returns. Somehow, his Why Did You Make Me Hit You? attitude and philosophical digressions on the nature of truth managed to be creepier than he could ever have been as a frothing sadist.
Being Human: Herrick is friendly, funny, and actually quite polite to the protagonists. On the face of it, Mitchell could do worse than have Herrick as a boss ... or a father. He's also a complete bastard plotting to Take Over the World. Towards the end of Season 1, he takes a turn to Faux Affably Evil.
The Bionic Woman: In the two-parter "Doomsday is Tomorrow", there's ALEX the supercomputer. He's trying to kill Jamie in order to prevent her from stopping his goal of a worldwide nuclear holocaust. But he's very polite, gives her fair warning of (most) of the traps he's set for her, and even regards her as something of a relation, given her bionics.
Boardwalk Empire: Nucky Thompson, the Treasury Secretary of Atlantic City and Villain Protagonist, is polite, funny, snarky, intelligent, and very progressive for his time (the 1920s). He's also such a corrupt politician that he supplies enough illegal liquor to incapacitate a bull elephant, and, while he usually seeks to avoid such confrontations, has no problem with killing those who cross him.
Bored to Death: Jonathan has a friendly conversation with a man holding a hostage. They end up smoking pot together before the cops break in.
Gus plays this almost to a fault. Not only are the employees at his chicken restaurant punctual and polite, but the people who run his massive underground drug empire are too. This is a man who fastidiously puts out snack trays before discussing multi-million-dollar drug deals with high-level Cartel players and invites his meth cook to a cozy home-cooked meal to discuss the finer points of family life. It makes the moments of real cruelty (slitting a man's throat unprovoked and threatening to murder Walt's family) all the more chilling.
Todd is mild-mannered, helpful, and completely sociopathic. There's a trope for what he does to make that last trait obvious, and it puts him in some pretty nasty company. What's especially scary is that he seems honestly confused that his associates can't simply shrug off the cold-blooded murder of an innocent child as a mildly unpleasant necessity or, at worst, an honest error in judgment the way he can.
Gale is friendly, eager to please, a gigantic dork and has never laid a hand on anyone as far as we know. He's also a professional meth cook who seems to view himself as Necessary Evil. Addicts are going to get their meth somewhere, so why shouldn't he give them the best possible product (and make loads of money in the process)?
Mike Ehrmantraut will happily have a drink with you before beating you down, and will calmly kill you without even raising his voice.
Brooklyn Nine-Nine: Doug Judy, the Pontiac Bandit. He's a manipulative liar and an unrepentant criminal, but he's also extremely charming and likable, and seems to genuinely love his mom.
Mayor Richard Wilkins III, who provides the page image. Actor Harry Groener, who portrayed him, claims to have based him in part on Ted Bundy: charming, able to talk you into anything, will kill you without blinking. Wilkins is friendly, mannerly, and is implied to be an upstanding, hard-working and (debateably) honest politician (Joss Whedon has admitted that Wilkins was intentionally portrayed as an efficient civil servant who authentically cared for his community, other than the entire "kill a bunch of high school students to fuel his ascension into demonhood" thing). He also provides well-meant (and, frankly, accurate) relationship advice to Buffy and Angel, inspired by his own marriage a century ago where she aged and died while he was immortal, and the exchange makes it obvious he did love her. He also genuinely cared for Faith, and while he was The Corrupter to her, Faith was already corrupted by the time she sided with him. By contrast she has fond memories of him into the rest of the series, seeing him as the only friend she's had who didn't try to manipulate or use her. And this was after her Heel-Face Turn. His status as basically a good guy — absent the "destroy the world" parts — was repeatedly lampshaded during the show, most brutally when they defeated him: the Mayor was destroyed because Buffy manipulated his finest quality — his paternal love for Faith. For all his evil, it was his sliver of goodness that did him in.
In fact, The Mayor was so polite and well-mannered, his Famous Last Words before being blown sky-high?
D'Hoffryn, master of the vengeance demons, seems to be a pretty nice guy, making conversation with Willow, showing up to Anya and Xander's wedding, etc. He got really nasty in his final appearance, though.
Sweet, the demon from the musical "Once More, with Feeling". He never even engages in physical violence. On the other hand, he can cause people to catch on fire, bring whole cities to ruin, tries to marry 15-year-old Dawn — and still has time to get a soft shoe in.
Halfrek, an evil vengeance demon, who is best friends with Anya and truly cares about her. She was the only person to notice how screwed up Dawn was in Season 6, and her raison d'être was enacting vengeance for mistreated children gives her the chance to deliver a truly epic "The Reason You Suck" Speech to the Scoobies because of it. It's honestly very sad when the previously mentioned D'Hoffryn murders her.
Anya. She's cheerful and quirky and bubbly, while reminiscing about the days when she had vengeance demon powers and flayed men alive.
Mr. Trick. Always smooth and cool, even when he's about to chomp on a hapless fast food employee (that he'd cheerfully conversed with just a few seconds before).
Clem, Spike (after his encounter with The Initiative), pretty much all the demons who showed up to Anya and Xander's wedding, Holden Webster from "Conversations With Dead People", and occasional random vamps. And Ethan Rayne.
Larry, a recurring character (yes, Dead Larry), is a consistently polite and cheerful man. He seems to truly care about his friends, tries to be a positive influence on the people around him, and will never do anything harmful to anyone without a good reason. He's also a remorseless sociopath, so "good reason" for Larry means "it would be marginally more convenient for me if you were dead". In his second appearance, Michael and Sam walk into Michael's house and are greeted warmly by Larry, who is very apologetic about the still-bleeding corpse on the floor, and makes himself as helpful as he can in dealing with the cartel that wants Michael dead. Well, actually, they want Larry dead, but he was using Michael's stolen identity at the time:
Sam: That guy sucks.
Children of the Stones: Rafael Hendrick , played by the very urbane Iain Cuthbertson, is polite, cultured, friendly, and brainwashes the villagers of Milbury into becoming "Happy Ones".
CSI: Dr. Dave from one episode. He's an elderly small town dentist, avuncular, well liked, very set in his routine, unfailingly kind to his patients and everyone else... and he's been torturing and murdering young women for decades.
The Daily Show: John Oliver made a comment in his Comedy Central stand-up special about how when Britain, in its imperial days, would conquer countries, but they would do it politely:
"And remember how we used to do it? We'd ring you up, tell you where the bomb was, when it was going to go off, and have a chat. How fucking polite were we!?"
Dexter Morgan, the title character of this Showtime show, exemplifies these qualities. His affability is his primary means of hiding his murderous outings. However, he sometimes dips into Faux Affably Evil territory.
He's not the only one. Many of the show's Big Bads also employ this method of keeping their second life a secret. In fact, one could argue that Dexter's rivals can be more charming than he is.
The Master, especially as portrayed by Roger Delgado. His later incarnations were a little less affable and a little more psychotic.
He wants the Doctor dead, but that doesn't mean he can't be friendly towards him. The Claws of Axos and The Sea Devils show this. Later incarnations don't even seem to want to kill him. Heck, his latest incarnation Created an army of Cybermen, and used nanoclouds to attempt to convert all the world's corpses into Cybermen, then have them kill all the living to create even more zombie Cybermen, with the intention of giving complete control of the army to The Doctor as a birthday present. As sick as it was, "she" in her own twisted mind, actually thought she was being nice. But at least she cared enough to remember his Birthday while The Doctor earlier admitted that he long long ago forgot when it was.
An even better example would be the Meddling Monk, another renegade Time Lord. A charming fellow who just wanted to "improve" history here and there...by blasting the Vikings with a thermonuclear bazooka, allowing Harold's forces to pwn the Normans at Hastings!!
Count Grendel of Gracht in "The Androids of Tara". Oh so polite, even as he outlines how he means to kill the Doctor and use Romana to get to the throne and then kill her.
Li H'sen Chang in "The Talons of Weng-Chiang". A superb illusionist, and a very charming fellow. He also hypnotizes young women and leads them to his fifty-first century war criminal master, who basically cannibalizes them.
Tilda and Tabby from "Paradise Towers", who are courteous and welcoming to passers-by, until they break out a knife to butcher the guest and cook them. It's a creepy affability, however.
Tobias Vaughn from "The Invasion". Very courteous, even to trespassers, as long as one is not hindering his plans. But when he gets upset...
Well IntentionedMagnificent BastardSir Charles Grover from "Invasion of the Dinosaurs". So courteous to everyone he meets, all the while planning to Ret Gone the Silurians and nearly all the human race in the name of Gaia.
Monarch from "Four to Doomsday", who carries a pleasant and civilized demeanor (which unfortunately wins over Adric for most of the last two episodes) despite looking like a giant crusty frog, and also wants to destroy everyone on Earth for its raw materials so he and his android army can travel back in time and meet himself "creating the universe".
Yvonne Hartman, head of Torchwood's now-ruined London branch, is such a thoroughly pleasant Benevolent Boss, it's easy to forget she's in charge of xenophobic scavengers with imperialistic ambitions.
The Slitheen, for the most part. They're only doing their business, after all, even if said business does involve destroying entire planets. Besides, hunting and killing are a trait of their species. They can't really help that. And they're pretty polite until you upset them. Though the Slitheen isn't the name of their species, but a large criminal family within that species.
The original Cybermen from The Tenth Planet. You see, their planet was dying, and they needed Earth to save it. It would destroy Earth instead, but that's no problem, we'll convert you all to Cybermen and you can come to Mondas. You'll have better technology, no disease, no fear or despair, and your lifespan will be dramatically increased! It's reasonable to say they weren't even evil. At worst, they treated the humans like children who didn't want to get their vaccinations. They honestly did not understand why anyone would reject their gift.
The new series Cybermen are less so, being far more Borg-like. "You will be upgraded" and "upgrading is compulsory" are pretty much the new "You will be assimilated" and "Resistance Is Futile". Ironic, as the Borg were often accused of being based on the Cybermen. However, what hasn't changed is that they still believe they're improving people, genuinely pitying the poor, emotional humans, and working to "free" them of that unenviable state.
Guess who turns out to be the Big Bad? Yeah, that's right, the ever-affable and fatherly Boyd Langton, who had seemed so much more moral than everyone else on the show since his transgressions against all that is decent and right in the world had merely been implied. It turns out he's really one of the two founders of the RossumCorporation. Even after he is revealed to the others to be their enemy, he is still friendly to them, claims to be very fond of all of them and to consider them his family, even though he still isn't reluctant to threaten them or kill the ones who get in his way.
EZStreets: Jimmy Murtha played by Joe Pantoliano is charming, funny and very scary.
Scorpius embodies this trope a good majority of the time he's on screen — particularly in keeping his minions rewarded and loyal. Even whilst performing horrific acts, his cool, personable demeanour remains...until you push him too far.
Another good example to be found in Farscape is Kaarvok, a one-off villain appearing in "Eat Me". Despite being a cannibalistic and badly-decomposed Mad Scientist with a penchant for cloning his prey to prolong his food supply, Kaarvok was eloquent, well-mannered, and almost charming if you could ignore the fact that his reedy English accent was emerging from one of the purest and most evil examples of horror on television.
Jaime is usually all smirks and witty remarks. He has a few friendly conversations with various characters, but can also be arrogant and casually condescending as well. Over the course of Season 3, he gets some character development.
Bronn is witty and charming, with a laid-back personality, but he's also a ruthless killer who will do just about anything for the right price. Sandor Clegane is particularly annoyed by the fact that Bronn can pretend to be a nice guy, while someone like Sandor must wear his brutality on his sleeve.
Get Smart: Siegfried. In one episode, he even joins forces with the heroes (at least, until the very end). Not so, however, in the 2008 remake film, in which he is stylish but not exactly friendly.
The Good Guys: The Tech Bandit from the episode "Common Enemies" of this Fox show. A nice fellow that only steals so that he can support his love of traveling and food blogging.
The Goodies: Played for Laughs in one episode which features Dr. Wolfgang von Petal, a Mad Scientist who just wants to be liked. Unfortunately for him, he seems to have a bit of a skewed idea of how to actually go about getting people to like him:
"All I've ever done is tried to help people! I helped the Russians with their nerve gas, I helped the Americans with their H-Bomb, I helped the British with their anthrax — I even helped the Nazis! Now how generous can you get?"
Hannibal: Since this NBC show takes place before the title character gets captured and imprisoned, we get to see him at his most affable: charming, well-dressed, well-mannered, and fond of inviting his friends over for dinner...and quite frequently, that hasn't even been a euphemism. He serves up exquisitely prepared meals in his gorgeous house wearing his wonderful clothes and makes pleasant conversation with his guests!
Healer has Kim Moon-Shik, the genial, genteel, caring elder brother and devoted husband of a newspaper magnate who rose from poverty to his present position, by betraying his True Companions and anything resembling principle, and abandoning a child who knew and trusted him personally, which he safeguards by loyally protecting the people who put him there and destroying anyone who gets in his way. He's so damn affable his own brother, who has been an eye-witness to some of his acts, has trouble believing he could go through with them.
Linderman is Affably Evil combined with Well-Intentioned Extremist. Particularly in his initial appearance, where he reveals that he likes cooking, as it relaxes him. When Nathan draws a gun on him, he says firmly, "Now you can't have any of my pot pie." In one season 3 episode, he is shown to deeply care about Angela, hating the mental abuse that Arthur has put on her all throughout their marriage. It's hard to believe that a guy who almost cried when trying to convince her to let him restore her memory would be the same guy who tried to blow up New York City and get Nathan into the White House to further his global ambitions.
Horrible Histories: Uses this approach on many characters, including Blackbeard, Emperor Elagabalus and Henry VIII. Incan warlord Pachacuti takes it to the extreme in a chipper pop video celebrating exactly how viciously he mutilated his enemies' bodies...complete with little bouncy skulls following the lyrics.
Kamen Rider Dragon Knight: General Xaviax, to the degree that if he'd come along earlier, this trope might've been named The Xaviax. What would you expect, though, from a guy whose entire MO is luring those capable of being Riders into a Deal with the Devil?
Abadon. Yes, a dude named Abadon is affably evil. It helps that we also see that Silas knows his weak point and convinces him to do the stabilizing, if not exactly right, thing for Gilboa even after years of imprisonment. He's played by Brian Cox. So in order to drive home that he's, y'know, evil — since he can't do much, locked up as he is — they have him remark offhandedly that when he was king and bored, he'd rape a serving girl.
Silas himself has more than a touch of this trope.
Law & Order: The Bernie Madoff lookalike and his wife are friendly and cheerful even as their assets are being seized and he's being arrested on suspicion of murder. He's innocent (of murder, anyway), and allowing himself to get caught was better than having his family killed by the South American gangsters he was cheating. The ending reveals the flip side of their affability: while the couple truly loved each other, they completely screwed their investors, childhood friends, and their own daughter out of their savings.
Lexx: Prince of Fire (later "Isambard Prince") could be best described as an Affably Evil, Card-Carrying Villain. Introduced as the de-facto ruler of the inhospitable desert planet Fire, he seems incredibly pleasant and unceasingly polite. He will unhesitatingly order the brutal deaths of his enemies and cheerily tell the protagonists that he's an evil and untrustworthy monster...right before offering them ''exactly'' what they want. And did we mention it's all but stated that he's Satan himself?
Long Way Round: A real life example was heavily hinted at, when Ewan MacGregor and Charley Boorman are put up for the night by a very friendly Russian "businessman" who always seemed to have a bunch of very large friends hanging around, and an unsettling number of assault weapons in his compound.
Ben Linus is affable and polite even when informing you exactly how terrible he's just made your life, and has only occasionally let out his scary side. Even when he does act scary, he usually waits a beat or two and returns to his affable demeanor with a small exhale or chuckle, which is much, much more frightening than if he were malevolent all the time. When he doesn't go back to being nice? Someone dies. Just call him Ben "I've Prepared You a Nice Breakfast Because the Next Few Weeks Will Be Very Unpleasant" Linus. This exchange from third season between Ben and Jack really says it all:
Ben: I'd like you to take a walk with me. Jack: You say that like you're not going to knock me out and put a bag over my head if I say no. Ben: Then don't say no.
Tom, aka Zeke, aka Mr. Friendly, earned the latter of those names from the fans because of his adherence to this trope.
Arturo: Is this the guy who hit you in the head with a bottle?
Tom: Yeah. I had it coming though.
Monty Python's Flying Circus: The first episode of Series 3 features a mass murderer who, when asked if he has anything to say to the court before his sentence is read, can only respond that he is terribly sorry — not only for his crimes, but for wasting the time and resources of the authorities and court, to say nothing of the poor jury that had to spend perfectly lovely days inside listening to accounts of his misdeeds. Though he's more than willing to take the punishment his crimes warrant, everyone (down to the police who apprehended him, but not before he badly injured them) is so touched by his apology that they decide to let him go free instead — and even sing "For He's a Jolly Good Fellow" in his honor!
Mystery Science Theater 3000: Even though they never forgot the purpose of their experiment, The Mads (and later Pearl) oftentimes have a strangely chummy relationship with Joel & Mike. In the Time Chasers episode, Pearl and Mike even hang out on her spacegoing Volkswagon van, enjoying a cuppa while chatting like neighbors on a front porch. "So, Pearl: why are you so evil?" "Hmm...I'm filled with hate, I don't know if that helps."
NCIS: Ari Haswari. He's always calm and polite, even when pointing a gun; he's charming and persuasive enough to convince several groups of his loyalty, which is truly only to his own agenda.
Neighbours: No matter what nasty (and sometimes downright evil) deeds Paul Robinson has planned, he will always do them with an air of debonair class.
Johnny Johnson, in a fifth-season story arc, exemplifies this trope. A rival businessman who takes over Mr. James' corporate empire (after hatching a secret plot to have the tycoon imprisoned for the infamous real-life "D.B. Cooper" skyjacking) succeeds in temporarily duping everybody at the station in to believing that his motives are good (even going so far as seducing Lisa, one of the main female characters), with the exception of Dave, the news director. When Dave calls Johnny on his evilness, he flat-out admits it, and says that he would be willing to give it up if Lisa were to marry him. Dave balks, to which Johnny replies, "I happen to have a talent for evil - doesn't mean I like it."
Jimmy James himself is not without his own misdeeds. While we never see him doing anything evil, he'll often commend his employees for engaging in duplicitous behavior (as long as it's good business practice), even when it's against him, as well as admitting (or heavily implying) to having done unethical things. The implications are that Jimmy may be a very friendly person, but he didn't get rich without all the standard business villainy.
Sayid (before his Heel-Face Turn) and Ryan O'Reilly. Ryan O'Reilly in particular, since his entire "Iago" gimmick requires him being able to charm the pants off of anyone to further his schemes.
Schillinger can be this at times, though how much is a facade is hard to determine. Keller is also pretty charming a lot of the time.
Person of Interest: Elias, the mafia don. He's generally very calm and polite, even with people who are about to kill him, and friendly with the main heroes even when they seriously inconvenience him. The two times he pulls a gun on Reese, he apologises for having to do it. Even his criminal acts are weirdly nice, like tightly regulating the illegal gun trade to keep a leash on violent crime, and sapping the ranks of the Russian mob by infiltrating their kids' school and being a really good teacher who inspires their kids to get out of the criminal life.
Power Rangers Ninja Storm: Lothor. Although he tends to be more comic-relief and Evil Is Dumb, he's probably the most lovable villain ever, mainly because of his character and the way his actor portrays him. The fact that he has two even more evil nieces (again, Evil Is Dumb) he has to look after only makes him even more affable.
Number 2, sometimes. It depends on which one you're talking about. The one played by Leo McKern certainly is. The main character's enemy is rarely a cackling villain; he's your friendly next-door neighbor who wants to read all your mail to make sure everything's okay.
Also Guy Doleman, Peter Wyngarde, and Georgina Cookson. None of them are ever unpleasant to Number Six.
Psych: Mr. Yin. Even when he's trying to kill Shawn, Gus, and Juliet, he does so in a way that makes it seem like he's just trying to help you out.
Satan himself appears affable, caring, and fatherly to Sam, his newest reaper, although his generosity is quite limited, and he quickly withdraws when Sam rebels. Despite his paternal attitude, he's no pushover.
He also never appears angry. The one time he is disappointed in Sam, he drops shelves full of heavy equipment on him.
Revolution: Major Tom Neville is the only militia person to be this. This is in contrast to the fact that just about everyone else in the Monroe Republic is a blood-thirsty Faux Affably Evil sociopathic killer. Be warned though that he can do villainous stuff, and he does not like it when people are rude to him. In episode 8, he and his wife Julia didn't hesitate to throw their friends the Fabers under the bus to save their son Jason. After the Nevilles leave the Monroe Republic in episode 13, Tom Neville seems to drop the "affable" part in episode 16 in favor of being a Jerkass and and a trash talker.
Sanctuary: Nikola Tesla loves Helen Magnus unconditionally, will do absolutely anything for her, and has always come through when the titular Sanctuary needs him. This does not stop him from wanting to Take Over the World, or constantly getting himself into trouble that he then needs the Sanctuary team to help get him out of. He's also one of the good guys (mostly).
Dr. Taylor Maddox, Kelso's temporary replacement as Chief of Medicine after his retirement. JD describes her as "an odd combination of super friendly and soulless".
Lord Oslek from Dr. Cox's story in "My Princess":
Dr. Cox: [narration] The dark lord Oslek was the evil ruler of the entire land.
Lord Oslek: Hey gang, how you holding up? [turns to the donkey-riding village idiot] That is a sharp-looking donkey.
The Shadow Line: Gatehouse. He's always scrupulously polite, and yet commits horrific acts of violence in pursuit of his goal.
Smallville: Lionel Luthor has no interest in hurting people pointlessly. As long as you're not in his way (and aren't related to him), you're in no danger. The same can be said of his daughter Tess Mercer, who eventually took over LuthorCorp; the same can not be said for his son Lex, or his Alternate Universecounterpart, Earth-2 Lionel, who are both classic examples of Bitch in Sheep's Clothing.
Stargate Atlantis: Todd the Wraith is surprisingly charming and personable for a life-sucking monster (and has a sense of humor — he even makes some jokes that aren't morbid), especially since every other member of his Always Chaotic Evil species seems to lean heavily towards the Large Ham school of Stupid Evil. He shows signs of being a budding Magnificent Bastard, and is honest enough not to pretend to be anything other than a human-eating monster, and is quite frank with the heroes in pointing out that, no matter how many times they cooperate out of necessity, their fundamental nature will inevitably make them enemies at some point (though the Atlantis expedition has begun to take steps to remedy this). Todd can even be said to be trustworthy, as he honors a deal with Sheppard even though Sheppard is completely at his mercy. He's also by far the most pragmatic of the Wraith.
Stargate SG-1: Baal, despite being rather sexist and genuinely malevolent, is at least fairly reasonable and relatively subtle compared to the rest of his megalomaniacal, Always Chaotic Evil, Large Ham species. He's one of the few Goa'uld who seems to understand that he's only pretending to be a god, rather than actually believing it. This was especially the case in the last few seasons, after he spent some time living as a human after losing his empire, and started to adopt Earth behavior and mannerisms (including talking like a normal person instead of in standard Goa'uld scary echo speak). In Stargate Continuum, Ba'al goes so far as to take over the galaxy using a fake "We Come in Peace" slogan instead of the typical "Kneel before Zod (or die)" approach. He even calls the U.S. President using a satellite phone, and invites him to lunch. He also promises Teal'c freedom for the Jaffa in exchange for his service, and even fully intends tokeep that promise.
The famous Khan Noonien Singh. It is often pointed out that once you strip away his limitless need to rule the universe, he's really a mirror image of Captain Kirk: polite, charming, a bit of a swaggering rogue. Then came the weird ear parasites, and the charm mostly vanished...
Kor, the Klingon commander from the first series episode "Errand Of Mercy". Even when ruling Organina with an iron fist, he has a sense of class about him, offering Kirk some brandy and showing a strong reluctance to turn what he sees as a Worthy Opponent into a mindless vegetable with his mind scanner.
The Cardassians tend to act this way when not obviously evil. This is especially true of Elim Garak and Gul Dukat. The former has pleasant chats with Bashir during which he often chastises the doctor for trusting him and praises him when he doesn't. Garak isn't so much evil as a pragmatic former spy who believes the ends justify the means. Gul Dukat, on the other hand, is a charming fellow who has many Pet the Dog moments, at times seeming like a Nazi with a heart of gold; however, his acts of villainy are malevolent and supervillainy. His heart may well be gold: cold and metallic. Then, there is the example of Picard's torturer, Gul Madred, who has some father-daughter time at the office and only really gets angry when the human proves so darn uncooperative. It would seem that Cardassian society does not condemn many acts we (and the Federation) might consider morally reprehensible, but also has many virtues we would find admirable—concern for children and the family foremost among them. Affably Evil almost seems to be the Cardassian hat.
Weyoun, also from Star Trek: Deep Space Nine, and the others of his species (the Vorta), who are the Founders' "carrot" race (with the Jem'Hadar as the "stick"). But Weyoun is the finest of them, genetically engineered to be efficient, evil, and oh so polite. And immune to most poisons (useful for a diplomat). Although he is specifically designed to be polite and persuasive, most characters (especially some of the Cardassians, who are supposedly on the same side) find him intensely irritating.
The Straits: Harry Montebello loves his daughter, is always polite to the police, and built a special set of steps so his cute, tiny dog can more easily get up onto his bed. He also is the head of a crime syndicate who will cheerfully have you stung to death by jellyfish if you cross him.
A Christmas Episode has the main characters encounter some festive gods, who pleasantly start to sacrifice the pair, while making polite conversation about Christmas traditions, tell Dean off for his potty mouth, and generally act like a sweet old couple making dinner.
Crowley, even more so as of "The Devil You Know". And so much more so after the Man Who Would Be King.
The Trickster/Gabriel is generally nice and playful and is genuinely respectful towards those who don't fit his standards for victims. In his original appearance both he and Dean admit to honestly liking each other. In "Changing Channels" he admits to Sam and Dean that he genuinely loves his brothers Lucifer and Michael and hates that he's going to have to see them killed. In "Hammer of the Gods" he undergoes a quasi-Heel-Face Turn and teams up with Sam and Dean against Lucifer. While he expresses no regret for his earlier murders and tortures, he's the one to defend humanity to Lucifer and reveal to Team Free Will Lucifer's weakness.
Eve, the Mother of All Monsters, behaves in a very kind and motherly manner and is genuinely protective of her creations.
The Archangel Michael is a Well-Intentioned Extremist who wishes to destroy half the world, but only because he believes it's God's will and what remains will be paradise. Other than that, he's generally kind, albeit arrogant. In "The Song Remains The Same", he politely tells Dean that Dean's attempts to defy him are futile, but promises to repair any damage done to Dean's body by having an Archangel possess him. Even his DragonZachariah is continually surprised by how forgiving Michael is of his failures.
The heroes from Gou Gou Sentai Boukenger had to face multiple villain groups. One of them was a ninja clan called Dark Shadow, who only cared getting rich by stealing priceless artifacts instead of conquering the world or exterminating humanity. Their main agent was a childish female ninja called Shizuka, who treated every mission like a game and had a playful rivalry with the blue ranger. She even gave him a motivational speech during the finale.
The Gaiark from Engine Sentai Go-onger are pretty much this. They are a race of robots out to pollute the earth. Their reason for doing it is because their race thrives in pollution, but can't survive in cleanness. If their goal didn't put them at odds with the Go-Ongers, they would probably get along fine, as they are a likable bunch. Certain episodes even show this by having both groups interact with each other hilariously. They also avert the trope You Have Failed Me and even compliment their minions at times.
Torchwood: Bilis Manger, the antagonist in the last two episodes of the first series. OK, he's a being of unknown origins who apparently has supernatural powers and is working to resurrect an ancient demon that feeds on the life force of all those who fall under its shadow. But he's a really nice old guy. And so classy.
True Blood: There's the vampire from The Authority who attached Bill and Eric's iCrosses: an adorably perky Wrench Wench who energetically explained how the harnesses worked, how they would kill them if they disobeyed The Authority, and that they were controlled through an iPhone app. "You boys are way too cute to be goo."
Senator Clay Davis is a blatantly corrupt, money-grubbing politician who will take anyone he can for as much money as he can. He's also friendly, charismatic, and cheerfully open about what he is:
"I'll take any motherfucker's money if he givin' it away!"
BrotherMouzone. You know, the man with the thick glasses, the dorky bowtie, the exceedingly polite speech, a love of Harpers magazine, and who has no problem shooting hoppers with hollow-point bullets or gunning down Stringer Bell!
Proposition Joe. Everybody likes him.
Wee-Bey Brice, The Brute of the Barksdale organization.
The X-Files: The Cigarette Smoking Man was this sometimes. Ever so polite and conversational until you get in his bad books, and he genuinely seemed to have a liking for Mulder, among others. The Well-Manicured Man could be classified under this trope too, but a good case can be made that he was never really particularly evil in the first place, especially by the time he died.