Neon Genesis Evangelion: Subverted in the manga version; Asuka is always nice to all the NERV staff, but with Shinji, Rei, Toji and Kensuke she is her usual, bitchy self. She keeps up this act for a while until, during a party, she punches out Toji in front of Misato after he starts revealing all her past angry outbursts. Misato then admits that they always knew that Asuka was faking her more amiable personality, prompting her to go ballistic... on Shinji.
Sayonara, Zetsubou-Sensei: Parodied with Mitama Mayo, who is evil, but because she also looks evil everyone who sees her decides not to prejudge and assumes she's not evil. Eventually even Itoshiki gets pulled into it, and decides there's nothing wrong with her.
Thriller Restaurant: In Episode 14, Anko's wart takes over her body and mind. The only ones who seem to notice anything wrong with her are her dog Kicchomu and Shou. Her parents actually become impressed by her personality makeover and maturity.
Xelloss of Slayers. Even though the whole party knows he's a demon, no one seems to mind him much - and that's despite his gruesome Kick the Dog record.
Slightly adverted as, once they know he's evil, they only keep him around because he's so strong and regularly helps them out, when it overlaps with his goals/ is bored.
Lampshaded: That Xellos is both incredibly strong and evil is terribly obvious to the viewer, but Lina and co. don't figure out he's a Mazoku until quite a ways into Next, when it's practically shoved in their faces. The only one who figured it out before hand? Gourry, who didn't say anything because he thought it was so obvious.
No-one ever trusted him to begin with, and indeed Xellos never seemed to actually try to be trustworthy either, introducing himself as "Xellos, the mysterious priest." As the characters note, "Who introduces THEMSELVES as 'the mysterious priest'?" It's just that being a rather more literal devil in plain sight never occurred to anyone but Gourry.
Nobody in Mai-Otome except for Chie seems to suspect anything of #2 Coral Tomoe, even though the latter's sarcastic tone of voice (and occasional smirk, even in front of the teachers) is often blatantly obvious.
To Nina, seeing Johan is like seeing pure evil. To everyone else, it's just seeing a blond pretty boy. At least until they see the light...
Gankutsuou: Let's see, the Count has long, sharp nails, pointed ears, fangs, his picture doesn't develop if he's photographed, has moments of cruel and disturbing behavior, oh yeah, and he's blue. Only one character ever calls attention to his odd features, and Albert can't understand why his friends could possibly suggest that the Count is evil.
Of course in The Count of Monte Cristo, people calling the Count a vampire is a continuously running joke. Even though he isn't blue.
An odd example: Mephisto Pheles of Blue Exorcist seems to be playing with this. It's difficult to tell at this point, but his first entrance drew immediate suspicion. He dressed extravagantly, wore all white, had dramatic mannerisms, and his looks made it obvious that he was a demon of some sort. Heck, even his nameis an obvious pun on that of a famous demon. But then this was subverted as it turned out that a lot of people have demon blood in the series, and some of them are exorcists. Then it turns out that he may be another one of Satan's sons - possibly his eldest, actually. Then again, the main character is also a son of Satan. So, Mephisto could still go either way at this point. He plays loads of "tricks" on his students, such as letting high-level demons on campus to challenge the potential exorcists (particularly Rin)which, he implies, is for the purpose of making them all stronger. But then he may have...some other reasons. The fandom suspicion only mounts the more "tricks" he plays, but there's still too much evidence to support the idea that he may genuinely want to bring peace to Assiah and Gehenna. He was in fact friends with Rin's adoptive father, and was responsible for sealing Rin's demon soul inside the demon sword when Rin was born. Really, he is pretty much the most mysterious character in the series at this point. It's highly possible that he is a Devil In Plain Sight but he may very well be a subversion of the trope. The fandom will have to wait and see.
Kumiko-san from Kamisama Kazoku plays this trope LITERALLY. Only Tenko gets to see her true face, and her stories are so outrageous that no-one believes her - least of all Kazoku.
In One Piece Ceasar Clown of the Punk Hazard arc is an Obviously Evil (he even has horns) Mad Scientist who specializes in weapons of mass destruction and regularly performs experiments on kidnapped children and his own subordinates. He has had nearly everyone around him convinced he's a paragon of virtue using a poorly executed combination of transparent lies, fake concern and Crocodile Tears.
The third movie has the main villain Count Butler. He even wears a coat that has the Kanji for EVIL written on his back, all while claiming he isn't evil.
Schneizel el Britannia from Code Geass can be considered one of these. He may be one of Britannia's most prominent royal figures, but masks his true intentions with apparently conciliatory actions, making him appear to be a Princely Young Man, managing to fool most everyone he comes across. Lelouch and Xingke are two notable exceptions. Of course, both have specific and personal reasons not to trust him. In addition, his father knows his real nature, and Suzaku just seems to assume that he's planning on killing his father, now that Zero is dead. Which he was indeed considering.
On the other hand, we've got Cecile and Euphemia who just seem to completely gloss over the fact that Schneizel's first appearance was him ordering their close friend and Euphemia's love interest and Knight, Suzaku, in holding down the main character while he fires deadly lasers at the both of them, with the expectation that Suzaku would die, after some shameless flattery towards the angry Cecile, as well as saying that he was sure that Suzaku would "somehow" survive, and Euphemia has other important things to worry about. Schneizel, himself, smiles and says that Suzaku shouldn't worry - he's not going to court-martial him. For not being killed by him. You have to wonder just how Schneizel can be this blatant, and not seem evil. I'm sure there is something kind of unacceptable about asking someone else's direct subordinates to die - for anyone other than the Emperor, at least.
Similarly, Clovis, despite his very short appearance. His public face and his actual ethics are very different. Not that any of his immediate subordinates care.
In Death Note, L sees something suspicious about LightYagami from the beginning, though nobody else seems to consider the possibility that the resident genius might also be the killer they're chasing - even as the detective they called in for the case tells them it's true. It helps that Light is a Magnificent Bastard and Consummate Liar, though; his villainy isn't really blatant to anybody but L.
Johnny the Homicidal Maniac: The title character commits ridiculously over-the-top mass murder and even himself seems puzzled why he hasn't been caught. It is later revealed that the reason why Johnny doesn't get caught is that he is a "waste-lock", a person created to watch over focal points of residue left over from negative human energy. This is revealed to him from none other than the Devil. It is implied, in the comic "I Feel Sick," that when the accumulated human waste acquires a mind of its own, it can allow a person to do whatever they want, even kill, without being caught. The doll tries to tempt Devi with this devil's deal.
I Luv Halloween. A black comedy of the darkest kind. About a group of amoral trick-or-treaters who want their Halloween candy even in the midst of an alien invasion and zombie apocalypse. One of the characters is Devil-lad, a hooded young boy wearing a devil's mask who patiently goes along with the group's crazy hijinks. The other trick-or-treaters note he smells like sulfur. Proven in the second volume, when he nonchalantly rises from a crater after being in the middle of a nuclear explosion. http://www.youtube.com/watch?v=qxDZ7DQmYwA&feature=related
Dr. Doom makes frequent attempts to take over the world that would be considered acts of war by real world standards, and most governments in the world just ignore him. No wonder he feels he better suited to rule the world.
This may count as Fridge Brilliance though: maybe world leaders have gotten the clue that all Doom wants is to keep having his little tiff with Reed Richards, so they just lay low and let the Fantastic Four deal with him to avoid getting targeted and devastated by Doom rather than just battered a bit in the crossfire.
Count Kasino in Les Légendaires. He's a young arrogant man who hires two assassins as his bodyguards, has a typical evil aristocrat face and attitude and is known by everyone to be a ruthless dictator on his own territory. He even has an evil grin when learning he has his chance to become king of Orchidia instead of his cousins Jadina and Tenebris. Yet, Vangelis actually seems surprised when learning it was him who attempted to kill Jadina and the Legendaries in the Gamera Mines. Partially subverted/inverted later however, as it turns out Kasino was actually nothing more than an Unwitting Pawn and the actual villain wasVangelis
Iznogoud: Comically inverted; Iznogood looks, acts and IS evil, he actually possesses almost all the deffect requiered to be a villain, and people of Bagdad are perfectly aware of his desire to overthrow the Caliph... but the Caliph himself never suspects a thing, instead seeing Iznogoud as a devoted, good, trustworthy friend. He even once admitted he often received anonymous letters trying to warn him about it, but never believed them. Ironically, the Caliph is the only person Iznogoud bothers acting good with.
The entire town in Little Sweetheart isn't just holding the Idiot Ball, they're firmly grasping the Idiot Ball. John Hurt's character, Robert Burger, practically has idiot ball hot glue gunned to him. His mistress, Dorothea, on the other hand, can tell that Thelma is not sweet, innocent, kind or anything but evil.
Harry Potter: Tom Riddle comes across as completely creepy and obviously sinister in both Chamber of Secrets and Half-Blood Prince, but he's completely trusted and well-liked by the teachers, especially by Slughorn. His creepiness in the films contrasts with the books, where he's stated and shown to be very charming as a young man and very good at presenting himself well.
Subverted given the ending, in that Patrick Bateman may have never killed anyone, and he's actually no worse than the company he keeps. And while Patrick is by no means a nice person - he is homophobic, racist, misogynistic, and tries to kill someone because their business card is nicer than his - his friends differ only in that they don't appear to be serial killers (though it would surprise no one if they were), making this less Devil in Plain Sight and more the Devil is Everyone.
The Black Hole: Dr. Reinhardt. Even though the "heroes" suspect, they don't suspect hard enough. What makes it even more jarring is Reinhardt's explicitly evil robot Dragon Maximilian, who manages to stir up little additional suspicion. (The title of this trope is justified by this horrifically bad movie's astonishingly bad closing sequence, by the way.)
There Will Be Blood: The main character is clearly one of these, complete with the Meaningful Name of Daniel Plainview. How much better his enemies the Sundays are is up to debate. At least until the bodies begin piling up.
Hot Fuzz: Simon Skinner, owner of the local supermarket. He often behaves extraordinarily creepy around Sergeant Nick Angel, having a bit of a Psychotic Smirk, making puns about killing and showing up around the murder scenes. The fact that the murders committed lead Angel to believe that Skinner is responsible in order to get more land for his supermarket doesn't help either (though that wasn't the true nature. Turns out Angel's only part right.)
Then there's the wonderful scene where Skinner drives up to a burnt down house with a song about fire playing loudly on his card radio.
In fact, every time Skinner turns up there's a song that's related to the murder. His drive past the scene of the "traffic collision" features Romeo and Juliet by Dire Straits.
John Milton: I'm the hand up Mona Lisa's skirt. I'm a surprise, Kevin. They don't see me coming: that's what you're missing.
Later on, he describes an encounter with one of his victims:
John Milton: There's this beautiful girl just fucked me 40 ways from Sunday... we're done, she's walking to the bathroom, she's trying to walk, she turns... she looks... it's me. Not the Trojan army just fucked her. Little ol' me. She gets this look on her face like: "How the hell did that happen?"
Cape Fear: This trope is the whole point of the film. It's even more obvious in the remake. At least in this case the local police did actually believe the protagonist's accusations, but were powerless anyway due to the antagonist being Dangerously Genre Savvy with regards to legal tricks he can use.
The remake of The Omen has this problem. Unlike the original, where Damien's angelic look was a striking contrast to his infernal nature, the new Damien is contantly frowning, glouting, generally creepy and has an "I-hate-you-all-and-hope-you-will-burn-for-all-eternity" look, just in case the marble statue in the third row might not catch up fast enough that he's the Antichrist.
The Dead Zone: A large part of the premise of Stephen King's novel.
Smerdyakov in The Brothers Karamazov is really just thought of as a scullion who has airs of intellectualism about him, and who carries blasphemous notions about religion. He's also thought of as pathetic to others because he suffers from epileptic seizures. The idea of him being the murderer is absurd to everyone in town for these reasons, yet he is. Only the protagonist seems to have any deep misgivings about him. I mean come on, he even flashes Psychotic Smirks whenever given the chance.
Until the last book, when the orphans are shocked to discover a community of adults who immediately perceive Count Olaf as both obviously in disguise and an untrustworthy villain. This comes with its own problems, of course, as they've already encountered "The Slippery Slope".
For extra effect, he dresses up like a stereotypical pirate, complete with a parrot on his shoulder.
Redwall: Reversed with Veil Sixclaw. Everyone except his foster-mother Bryony realises that he's a delinquent and guess that it was him when an Abbeydweller is nearly killed. Ironically, it's heavily implied that if they'd treated him as if he was normal, he'd have grown up okay. But then they aremice trying to raise a ferret.
Harry Potter: This is inverted in the novels. Harry is utterly convinced that Snape is a terrible villain, but nobody believes him except his friends. Eventually, even they stop believing him. This continues until Snape kills Dumbledore, but is then subverted again when it is revealed that this was a mercy killing, agreed to well in advance, due to Dumbledore suffering under a terrible, incurable, and fatal curse.
Played straight with Draco Malfoy in Half-Blood Prince. That is, nobody thinks he's a good guy, but everybody except Harry stubbornly refuse to believe that a son of the enemy second-in-command might've actually followed in his daddy's steps.
'The Demon Princes'': The titular villains from Jack Vance's series, despite being infamous pirate lords and criminal bosses, value their anonymity and are essentially this. One has a position at a prestigious university, and on one occasion the hero Kirth Gersen gets into a bar fight with a Demon Prince without knowing. Often, the most difficult thing for Gersen is just figuring out who the Demon Prince is.
A Song of Ice and Fire: How anyone in Westeros could ever trust Roose Bolton, lord of the Dreadfort, is shocking. The man's sigil is a flayed man, he comes from a family with a long standing tradition of skinning their enemies alive and wearing their skins in battle, he always speaks in a Creepy Monotone and his favorite pastime is getting leeched. Granted, everyone finds him a little unsettling but still, he's relied upon to perform extremely important roles several times. Trusting him never turns out well
Petyr "Littlefinger" Baelish is obviously up to no good from the moment he appears in A Game Of Thrones and even tells Ned Stark not to trust him. When Ned does trust him, he betrays Ned, to no one's surprise. In the next two novels, where Littlefinger interacts with the Lannisters/the Deadly Decadent Court, mostly everyone seems to think that Littlefinger is just some ambitious commoner who wants to be a lord, and only Tyrion gets how much of a ruthless and dangerous backstabber he really is, or so he thinks. Even Tyrion never imagined that Littlefinger was essentially the Big Bad who deliberately engineered the civil war engulging the continent, and orchestrated the murder of Jon Arryn that kicked off the plot. He still doesn't know that, in fact- Baelish only confessed it in a Motive Rant to his hostage/protege Sansa Stark, and he is doing it for the sake of power and is well on his way to becoming the most powerful man in the realm. He's probably holding stuff back from her too.
Everyone in Krabat should recognize Pumphutt for his big hat immediately, but they never do until he tells them who he is. Can be explained with A Wizard Did It.
Sherlock Holmes: Professor Moriarty. Three layers there: his obscurity, his charm, and his crack legal team. The brass tacks are pretty much reserved for the normal course of business in that massive criminal empire he's running, until Holmes manages to get him into a bind.
In Michael Kurland's The Unicorn Girl, Michael visits a universe where most of the people literally cannot see naked people, which leads to much confusion when some naked thieves begin to steal from people at a dinner party. Michael watches dumbfounded as his hosts are robbed right in front of his eyes, and when he tries to point it out, he ends up getting blamed for the crime himself. Fortunately, he realizes there's an obvious way to escape...
Dr. Hannibal Lecter was this, being a well known psychiatrist, cook and supporter of the arts. Nobody suspected he was the depraved and thoroughly insane serial killer known as "The Chesapeake Ripper." His arrest and outing as a cannibal resulted in a scandal.
Played for all its worth by Sinistrad in The Death Gate Cycle. As a young man, he knew he was getting a reputation among other mysteriarchs for being an Evil Sorcerer, so instead of trying to hide his behavior he played it up (to the point of changing his name to "Sinistrad") to such a level that he was dismissed as merely a harmless eccentric (he also seduced and married a beautiful, idealistic young sorceress to add to the impression that he really wasn't so bad underneath his "cliché evil wizard" schtick). That allowed him to quietly build up his power and finally take over as head mysteriarch before anyone quite processed that yes, he really was that dangerous after all.
Duke Roger in Song of the Lioness. He's quite charming, but Alanna thinks he's a little off and he has a habit of goading Jon to do dangerous things or engineer danger for him (like a plague or a Uriah Gambit) along with sending a couple of Animal Assassins after Alanna... but everyone else adores him, including Jon. We learn at the end of the second book that Roger has magically protected himself from suspicion.
In Charlie and the Chocolate Factory the Bucket family, especially the grandparents, is dismayed to learn that each of the first four Golden Ticket finders is repulsive in their own way (in order — gluttonous, greedy, proud/rude, slothful. Yet they are all indulged by their parents and acclaimed and celebrated for their luck, which isn't even really luck in Veruca's case, by the rest of the world. The four kids get a very rude awakening to their own faults once they're in the factory, because — while he may not show it at first — Willy Wonka, to say nothing of his Oompa-Loompas, does recognize them for who they are and has No Sympathy for what happens to them when they give in to their vices and meet dreadful fates.
Live Action TV
Leave It to Beaver: The iconic television DiPS: Eddie Haskell. Prim and polite to adults, a bullying troublemaker to everyone else. Ward Cleaver to June: "There's something odd about that boy." Beaver to Eddie: "Even Wally doesn't like you, Eddie, and he's your best friend."
The film revealed that Mrs. Cleaver knew about Eddie all along.
The film? She had him pegged from day one: "I just don't trust a thirteen-year-old boy who's that polite."
Dexter works in the homicide department of the Miami police department by day, and kills by night; despite this, he stays well under everyone else's "something's not right with him" radar, except for Doakes. Dexter comments at one point about being in a room full of police officers and Doakes being the only one who has any sort of sense of something wrong about him.
Done again in Season 3 with Miguel Prada, the local DA, who only Dexter suspects of sinister urges. It turns out that Dexter underestimates the degree of his sociopathy and has to kill him.
The '80s sitcom It's Your Move featured Jason Bateman as a manipulative teenaged con artist whose single mom was (initially, at least) blissfully unaware of his intrigues. The first dozen or so episodes dealt with his efforts to prevent the mother's equally devious boyfriend from exposing him. When she finally got wise to him, the show's whole comedic premise was effectively retooled (and, arguably, ruined).
Dollhouse: Laurence Dominic. In episode 5, he tries to kill Echo. In episode 9, he is revealed to be the mole. Note that at the time of the episode's airing, the Dollhouse WMG page had eight different guesses eight guesses as to the identity of the mole, only one of which was a repeat, and yet no one had bothered to guess that it was Dominic. Because we're too Genre Savvy to fall for such an obviousRed Herring...yeah.
And then it turns out he wasn't so much a "devil;" he saw himself as protecting the Dollhouse AND protecting the world from the technology it used. His negative convictions turned out to be right. Nobody important in the House figured that out until too late.
Oddly enough, the Devil in Reaper frequently exemplifies this trope.
Subverted and parodied in the Blackadder Goes Forth episode "General Hospital"; a German spy has infiltrated a nearby field hospital and Blackadder is assigned to find out who it is. In the field hospital, he meets a wounded man with a German accent so thick it could be spread on bread ("My name... eeeees Meeeiiiister... Smeeeeth.") who's always skulking around acting suspicious. Turns out he is a spy... a British spy, who's been undercover in Germany so long he's picked up "a teensy bit of an accent", and was even the one who informed Melchett there was a spy there in the first place. Blackadder even lampshades how ludicrous it would be for the Germans to place in a British field hospital a spy with a thick German accent. This doesn't stop Darling from humiliating himself by trying to arrest him, however, or George from blithely asking him whether he had seen any spies in the hospital (and this was not George being clever enough to realise that the man with a strong accent couldn't be a spy, he was simply too thick to notice it).
Also done literally in the The Black Adder episode, Witchsmeller Pursuivant. When Prince Edmund is accused by the titular Witchsmeller of being a witch, during his trial, he calls a random peasant woman to testify against Edmund, and who claims she bore his son, which the Witchsmeller claims is "the son of Satan." He then asks the people watching the trial if they can "see this son of Satan anywhere in this room?" When the camera shows the people looking at the person next to them to see who it is, it shows what clearly looks like a Devil at 2:04, but no-one apparently realises this.
From Merlin, Agravaine, who waltzes around Camelot in a forbidding all-black outfit and Severus Snape's hairstyle, frequently flashing Psychotic Smirks when nobody's looking and popping off to visit Morgana at regular intervals. Merlin and Gaius quickly peg him as a villain, but can't say anything due to him being Arthur's uncle and chief advisor, and therefore above reproach without serious evidence.
Mr. Morden in Babylon 5. In his first appearance, he's faultlessly polite, and even does an unasked-for favor for Ambassador Mollari ...and yet he's got an unsettling and even sinister air about him that clearly marks him as "evil". Only Kosh and Delenn recognize him for what he is that first time (and it takes a moment for Delenn), and by "The Coming of Shadows" in Season 2, Vir has also realized that Morden is trouble (relatively quickly, as Vir didn't even know about Morden until the last episode of season 1).
In Breaking Bad, this is the modus operandi for many of the major players in the drug industry.
Saul Goodman, the Amoral Attorney of the industry, places cheesy adverts on benches and TV channels, appearing as a cheap and unscrupulous Ambulance Chaser instead of the hyper-competent law-breaker he is.
Gustavo Fring, the biggest boss in the Albuquerque-area drug trade, raises money and galas for his adversaries in the Drug Enforcement Administration, is a very public pillar of the community, and is commonly seen at his (legitimate) businesses overseeing operations as a Benevolent Boss.
The protagonist, Walter White himself, keeps his job as a high school teacher and continues hanging out with his DEA brother-in-law, despite getting deeper into the drug trade.
Eminem contributes these lines to Dr. Dre's "Forgot About Dre":
And when the cops came through, me and Dre stood next to a burnt-down house
With a can full of gas and a hand full of matches, and still weren't found out
Gary Smith in Bully. Despite how often he's told lies in the past, everyone still takes his word for it, apart from Jimmy and Pete.
Zola Dane from Drakan: The Ancient Gates. Bad foreshadowing, gesticulations, and voice acting (not to mention if you actually talk to him before going to the Shadowmire) make it an Un Reveal when you have to kick his butt the first time.
Damon Gant, Morgan Fey and Kristoph Gavin are better disguised versions, but still obviously bad people.
And Matt Engarde is a much better disguised version. Also his butler, aka Shelly De Killer.
Most culprits have a bad habit of turning into this as the trial goes on, suffering Freak Outs when Phoenix has them on the ropes and openly gloating when they have the upper hand, to the point that, if they were being judged by a real-life jury, most of them would probably be convicted just by how suspicious they're acting. It's implied this very thing might have happened at the end of case 4-4 to Kristoph Gavin, as the new (or, in North America, revived) Jurist System was a key part of that trial.
Assassin's Creed: Al-Mualim. Despite every target telling Altair he's lying or using him and there never being any explanations for anything, everyone pretends to be surprised when he turns out to be the Big Bad.
Actually both games have a whole bunch of examples. Atris also in the second game, and if the player goes evil, other characters mistake them as such. And then there's the player in the first game, with a twist. Bastila sort of counts too, since it's obvious going to go evil from the start, although she doesn't really qualify as she was turned later on. And Revan and Malak, back when they were Jedi (and everyone who turned with them).
In Wallace & Gromit's Grand Adventures: The Last Resort, Ms. Flit's cutesy dogs Poodgie-Woo and Tinkie-Wee are quickly revealed to be ill-tempered, mischievous mongrels with a collective mean streak twice as long as your arm.
Michelle in Grand Theft Auto IV. From the newly bought furniture to her not really answering Niko's questions as to what she does to her near-constant questions asking if Niko and friends are involved in crime, it's pretty obvious that she's really an undercover government agent...well, obvious to everyone except for the in-game characters. Although Niko does occasionally comment "There's something strange about that girl..." right after they have sex.
Dragon Age: Origins: Teyrn Loghain was painfully obvious. Though everyone trusts him because he placed the blame on the Grey Wardens and was also a national hero for freeing the kingdom from decades of foreign occupation. The former can also be said of Arl Howe.
Arl Howe was voiced by Tim Curry.
Other than being voiced by Tim Curry, though, you probably wouldn't be expecting him to be a bad guy. At first.
In Dragon Age II, Mother Petrice. Tell me you didn't look at that cold, piercing gaze and at least predict she'd be a Smug Snake.
Also Bartrand. Listening to him you wonder why anyone works for him, why Varric hasn't abandoned him, and why Hawke and the rest of the group don't just shoot him on sight. It would have saved a lot of trouble.
In Mass Effect 3, Councilor Odina turns out to be allied with Cerberus, when up to this point he was merely a smug self-serving politician. Ironically, the third game largely makes him more sympathetic and cooperative to Shepard than he ever was in the previous games, up until The Reveal.
The third line of dialogue from Chancellor Cole in Zelda Spirit Tracks includes an ominous prediction while he stares at you with an insane evil smile. If you are still surprised when he shows himself as the Big Bad of the game five minutes later, you should start getting worried.
The scientist, Kindjal of Custom Robo Arena. She was so obviously a villain the second you saw her sprite.
From Custom Robo for the Gamecube, there is Evil, a flamboyantly overdressed nemesis to the player and the Steel Hearts...he seems more like a Smug Snake who exists to beat the Steel Hearts to all the good jobs, at first. While it stuns the cast when he declares his true intentions, it's no surprise to the player when he defects to the Z Syndicate with a Robo that will destroy the world to try and gain favor with the Z-twins. Love Makes You StupidEvil.
Jan Rosencrantz in Vagrant Story. Everyone knows he's a traitor and an all-round bastard. It's just that no one cares. He turns out to be more powerful and ambitious than the characters had anticipated.
Ironically though, even if you do realize that, he's actually a pretty nice guy personality wise, and in some games he has a really strong claim to being considered a good guy anyway, especially compared to just how Eviler than Thou his competition can be.
In The Elder Scrolls IV: Oblivion, one of missions you can do for the local assassins' guild involves you, around a half-dozen of poor saps who become your victims, and a house locked from the outside. Funny thing is, you have the choice of telling one of your victims that you are the assassin right before you off everyone (though she just laughs it off). Add that to the fact that you are the only one who can wears armor or weapons just screams, "I'm an assassin!"
When you enter the house, you can't be wearing armor or have weapons drawn. Also, after two or three deaths, at least one of the characters dons armor or finds a weapon.
Kingdom Hearts: Birth by Sleep: Master Xehanort might as well be carrying a neon sign reading "I am evil, nyahahaha". Nobody, other than Yen Sid, seems to notice, not even the guy who fought him once before in a battle of light against darkness.
In World of Warcraft, Onyxia posed as Lady Katrana Prestor in order to give the very young king Anduin Wrynn bad advice that kept Stormwind weak.
In Syndicate (2012), application of "datascape camouflage" allows you to walk around secure places without anyone batting an eye at the sinister masked man in the black coat. Naturally, it fails at the worst possible times.
Sword of Mana shows us that people will readily follow and have no problem with a guy who names himself Dark Lord.
Miho in Megatokyo fits this trope, at least if you ask Largo.
In Sinfest, quite literally. He takes Cerberus out for walks around the neighborhood and flicks off God from hilltops. At the same time, God regularly speaks to people in the form of giant hand puppets in the sky.
Satan And Me has a scene where the Devil bares fangs and a snake-like tongue in a crowded makeup store, but only one person seems to notice.
And Alex Brisbane, Mr "I'm Most Definitely Not a Villain". Fortunately he only has to trick Tristan, Tea, Joey and Yugi, which isn't exactly difficult.
And then there's Marik Ishtar "Malik Blishtar"...
Joey: [thinking] I still think there's something fishy about that guy...
Marik: Wahahaha! Destroy you all!
Joey: [thinking] Man, if I could only put my finger on it...
In A Very Potter Musical, Quirrell/Voldemort are played by two people standing back-to-back in the same set of robes. Quirrel's turban covers Voldemort's head, but it looks exactly like what it is: a second head, covered by a turban. Also, the turban occasionally sneezes. Needless to say, this is played for laughs.
Also played for laughs in one video of The Spoony Experiment where Dr. Insano ran for president... and won.
Dr. Insano: My advisor was Fu Manchu for God's sake, how can you be this STUPID!?! (insane giggling laughter)
Whateley Universe: Don Sebastiano — that's his chosen codename. I mean, he's known as 'The Don', he turned two teenagers into mindslaves last year, and he's still walking around campus as the head of the Alphas. Yet no one in the school administration seems to realize how badly he needs to be stopped.
Actually, they DO know.... even the Headmistress is fully aware. But they're keeping him on because he is the only link they have to the real, as of yet unknown, mastermind behind his actions....
The Cinema Snob is particularly irritated by Driller Killer's lack of subtlety with regard to who the slasher is.
Exaggerated in To Boldly Flee. Mechakara is this from the start: his voice noticeably synthesized and he acts completely differently from Linkara. Then he assimilates the Nostalgia Chick, and she looks like Seven of Nine, her voice is even more synthesized, and she starts using Robo Speak. And then he assimilates Todd, who becomes Robocop. Most of them still don't notice.
Dib has apparently cried wolf so many times that the rest of the class seems to ignore the obvious signs to spite him (also because their world is full of ridiculous people like Old Kid and because everyone is remarkably stupid). This is one of the primary reasons for fans of the show Rooting for the Empire. Its hard to support the human race when they are - almost completely - Too Dumb to Live and the prime example of the show's Crapsack World.
"It's like they want to be destroyed!"
The only other person who knows Zim for what he truly is, is Dib's scary sister, Gaz. But she doesn't lift a finger, since she believes Zim is too stupid for his schemes to work. And most of the time she's right.
Angelica of Rugrats, though occasionally she did get caught. Her role was eventually trumped by Savannah Shane in both Rugrats Preschool Daze and All Grown Up!. However, unlike Angelica, she has yet to receive any real comeuppance or consequences.
Jessica Lovejoy from one episode of The Simpsons. Her parents (the local minister and his wife) know that she's a troublemaker, but consistently look the other way because they do not want to bring disgrace upon the Lovejoy family. This allows Jessica to be both this trope and a Bitch in Sheep's Clothing - and to frame innocent boyfriends (in this case, Bart) for her many misdeeds.
Joe from Moral Orel is an all around hellion and sociopath, yet nobody with the exception of the main character seems to make much of a fuss about it.
Soundwave of Transformers Animated definitely fits this troup in his premiere episode. Bulkhead spends half the episode trying to convince everyone else that the robot is evil. Guess who was right.
Longarm also fits, given that he was hinted the entirety of "Autoboot Camp" to be The Mole. The fact that he was actually Shockwave in disguise, we didn't see coming.
The anonymous bunny in the Ruby Gloom episode "Bad Hare Day".
A bunch of mind-bendingly cute animals from an episode of the Powerpuff Girls. Although it's not as if anybody didn't notice that they robbed banks, but rather that everybody (sans the Girls) was mesmerised by their prettiness and fuzzyness and was willing to give away everything they demanded, that is money, gems and the city key of Townsville.
The Fairly Oddparents: Vicky is constantly left in charge of Timmy despite obviously being a malicious monster.
Inverted in that Timmy's parents are the only ones who don't notice that Vicky is evil. They eventually do find out she's evil, but it gets Reset Buttoned because it's that kind of show.
Dad: Now Chip Skylark's hit song "Icky Vicky" finally makes sense!
Doug Dimmadome: Well, what did you think that song was about? Pumpkins?!
The Golden Eagle Twins in El Tigre: The Adventures of Manny Rivera. Two twins who take advantage of their superhero fame to scam the locals into getting whatever they want. Only Manny and Frida are aware of this.
Cartman from South Park. In many ways, this trope is averted: after all, most of the characters know just how horrible he is. That said, Stan and Kyle oftentimes get punished right alongside him, despite being generally good kids who are usually trying to stop whatever evil scheme he has going. This becomes especially painful (not to mention a Downer Ending) in "Toilet Paper," in which they're given much harsher punishments despite being genuinely apologetic—unlike Cartman, who only apologized so they would get most of the blame.
The best example on Southpark, which is lampshaded, is the episode "Cartman's Incredible Gift". In the episode, Cartman pretends to have psychic powers and the police blindly listen to whatever he says, ignoring important evidence. Kyle suspects a disturbed man to be a vicious serial killer (he is) and tries to tell the police about him but they are completely blind to the killer's suspicious behavior and mannerisms and make no attempt to bring him in for questioning.
G.I. Joe: Renegades: The newest incarnation of Cobra has the ruthless terrorist organization posing as a benevolent corporation providing essentials such as defense technology, pharmaceuticals, retail outlets, and apple pie. Their corporate logo not only bares a casual resemblance to the classic "hooded cobra" symbol of the original, it also closely resembles the Greek letter "Omega". Add to that, the CEO "Adam Decobray" has never been seen in public, and even putting on his best nice-guy voice in video conferences, he still sounds like the creepiest, most sinister man that ever lived (as opposed the to horror it really is) thanks to Charlie Adler's fiendishly subtle acting.
Vertex in Rollbots. In one episode, he is in a disguise (which is about as sinister as when undisguised) and directly has a conversation with Pounder and Aria of all people, right in front of Spin, the one person who knows the truth about him.
Zig-Zagged in the season two finale of My Little Pony: Friendship Is Magic. Twilight Sparkle assumes Princess Cadence is evil, namely because she didn't respond to her Secret Handshake, and how she (Cadence) mistreats her friends. She tries to warn her friends, but they simply wave it off, and her last attempt causes them to leave her in disgust. It isn't until Twilight arrives with the real Cadence that she is sorta proven right. But by then, the Changeling impersonating Cadence had already become too powerful to stop.
Ultimate Spider-Man: Spider-man had no idea that Norman Osborn is the one who put a price on his head and is obsessed in capturing. In which case there were some Flashback Cuts showing him to busy hanging out with Harry, and is oblivious to Norman destroying pictures of Spidey who is right in front of him.