Nestle Quik introduces us to kids who think the lady in the spooky house is a witch who doesn't like children: "NOT THE WITCH!!!"
Anime and Manga
Sakaki from Azumanga Daioh is a less extreme example, since she doesn't come off as evil upon first glance, just a bit intimidating. She still hits the high points, though, being introduced as an intimidating enigma (the girls, for example, initially believe the scratches and bruises she gets when trying to pet Kamineko are because she's a Delinquent who likes picking fights) , but revealed rather quickly to be a Gentle Giant.
Ouran High School Host Club has Bossa NovaCasanovaKasanoda. He's the son and heir to a powerful Yakuza family who has been raised to act aloof and intimidating, and he just looks like a scary guy. He's known as the Human Blizzard by most of the student body. The truth is, he's really a Gentle Giant with a love for animals. Unfortunately, his mean-looking face frightens animals he tries to help, so he settles for taking care of plants instead.
Ouran also gives us Nekozawa, the president of the Black Magic Club. He's often seen wearing a black hooded cape and staying in the shadows, creeping out the other characters. We later find out this is because he is extremely sensitive to light. He's really a considerate person and wants to be a better brother to his little sister, even taking lessons from the Host Club so he could fulfill her fantasy of a princely big brother.
Fullmetal Alchemist: Somewhat like the above is Sig Curtis, the husband of Grade-A BadassAction Would-Be Mom Izumi Curtis. Despite the fact that he frightens children with this incredibly scary face (which he lampshades in the same scene), huge frame, and booming voice, and is for the most part completely asocial, he's a pretty nice guy.
Alistair Krory III from D.Gray-Man fits this trope to a T. He lives in a spooky house with mutant plants and eats villagers. Doesn't help that he really LOOKS like a vampire. Turns out that his victims are demons in disguise anyway and he's really a good guy.
Angel Beats!: Tenshi/Kanade Tachibana. She's seen as a freak because she doesn't have any friends, but that's only because she's actively trying to graduate those around her, and thus is never really seen with anyone for any length of time.
Sawako of Kimi ni Todoke looks frightening to her classmates who therefore avoid her, which prevents her from developing social skills, which causes her classmates to avoid her even more in a vicious cycle of high school drama. Turns out she's perfectly sweet and sincerely cares for everyone despite how they treat her. This becomes apparent when she gains the courage to make lasting relationships, becoming a valued member of her friend group.
Naruto: Gaara is an interesting example. He plays this trope straight as a young child; he just wanted to have friends, and personally brings medicine to a child he (accidentally) hurt. Then he crosses the Despair Event Horizon and becomes a Serial Killer. Finally, he gets some sense beaten into him by Naruto and eventually becomes Kazekage. However, because of his checkered past, there are people in the Sand Village who don't trust him, and he still doesn't have too many close friends. (And the ones he does have are mostly concentrated in the Leaf Village.)
One Time Skip later, however, and Gaara is not only reformed enough to stand equally with every other Kage, but leads them and the entire goddamn Shinobi world in the war against Big Bad Tobi.
The spirit in Ch 2 of Helen ESP, who keeps stopping the elevator at an empty floor and looks like a shadow ends up saving Helen from a rape attempt.
Addie Clark, a.k.a. "The Governess", from Bizenghast is a posthumous example. When the series began, Addie was one of the ghosts who haunted Dinah's home, which was originally a school and before that a hospital which had burned down. It's been implied that Addie had been responsible for killing numerous children when the house was St. Lyman's School for Boys, and disappeared after supposedly setting the fire that destroyed the school. Over the years Addie's ghost was particularly cruel to Dinah. Volume six and seven revealed that Addie was nowhere near the monster she'd been made out to be. A kind, young school teacher who made an effort to watch over the younger students who were bullied, she witnessed the people of Bizenghast hang a young woman as a witch one night. One of the men at the hanging was St. Lyman's headmaster, and he knew Addie witnessed the whole thing. She tried to get a letter to her sister explaining the situation by hiding it in a painting, but it never reached her. The headmaster tried to silence Addie by trapping her in the hidden cellar she sometimes taught her students in, suffocating her with smoke that accidentally turned into the fire that destroyed the school. Addie died in a closet along with two young boys. After Dinah discovered the bodies and the letter, Addie's ghost was able to come back to its senses. Apparently, because people had believed the rumors that she was a monster, this warped Addie after she died, and the truth being revealed was enough to give her back her clarity.
On the surface Haruka from Kotoura-san may look like a rude, freaky jerkass who blurts out other people's secrets, but that's only a Jerkass Façade she cultivated after passing the Despair Event Horizon far too many times and genuinely thought herself as a freak who would hurt anyone she cares about. Deep down she is more similar to a conventional moe heroine.
Hotaru Tomoe aka Sailor Saturn from Sailor Moon. Not only does she have strange healing powers, she often lapses into "seizures" that are the result of the alien entity Mistress 9 taking control of her body. During these episodes, she blacks out and often unwittingly commits harm to those around her. Because of this, her classmates fear and reject her. In reality, Hotaru is a very sweet and gentle girl who is terrified of hurting anybody and wants nothing more than to have a friend.
Spirited Away: Despite initial impressions, neither Yubaba nor Zeniba are all that evil. Neither is No Face, who is seen only by himself, and tells Chihiro/Sen that he is lonely and doesn't have any friends or family.
Both protagonists in Tucker & Dale Vs. Evil, who are mistaken as serial killers at first by a bunch of paranoid college students. Dale especially falls under this category, as he is a Gentle Giant who would never hurt a fly, except to defend a loved one.
Nell Kellty is neither a Wild Child, psychotic, autistic, nor mentally retarded — all of which are ascribed to her at various points in the film. In fact, nearly every assumption others make about her (and her family) turns out to be wrong.
Toy Story: Sid's mishmash toys. They look terrifying and appear to be cannibals when they assault a dolly Sid mutilated, but when they later assault an incapacitated Buzz, they actually mend him... just as they did with the dolly (who turns out to be fine). It's a safe bet they look like they do because they didn't have all their parts when they reassembled each other the first time, and had to make do with what they could find. In some cases they were now their own toys thanks to Sid and for some like Legs a full repair would be fatal.
Get Low: The rumors about Felix Bush are partly deserved, but only because he tends to shoot at anyone who comes near his property. However the opening scene has him catch one of the children who destroyed his window (throwing up on Felix's shoes in fear when caught)...and just patting the boy on the shoulder and letting him go. Yes, he is a Jerk with a Heart of Gold, but the Jerk part only came after years of beingtreated as an outcast.
The Journey Of Natty Gann: Natty assumes the worst of Charlie the blacksmith (not entirely without reason, as he took her Canine Companion away chained up in a crate) and approaches him only with a shovel in hand and considerable trepidation, because he's a big, scary-looking guy with a badly scarred face. She soon discovers, however, that he's a kindly soul who intended all along to release Wolf back into the wild, and after she tells him her story, he gives her food and money for a train ticket and wishes her and Wolf well.
The Sandlot: James Earl Jones' character exemplifies this - an ill-kept yard and a seemingly vicious dog keep the neighborhood kids at bay, but he's actually an avid baseball fan who was willing to trade a mint-condition baseball with all the signatures of the 1920s "Murderer's Row" Yankees for the now-mauled one that Babe Ruth had signed.
The title character from Wreck-It Ralph. Poor fellow lost his home, lives in the dump, and wrecks and apartment because it's his job. The "Nicelanders" treat him like trash even when he's off the clock, with the exception of Felix. Little wonder he finds a kindred spirit in the form of a Dummied OutBratty Half-Pint in a sugar-fueled racing game.
Doc Brown in Back to the Future, who was labelled as a dangerous lunatic by many people in Hill Valley ever since an experiment-gone-awry caused his family mansion to burn down in the 1960's and forced him to move into his garage. In reality however, he's an incredibly friendly, albeit eccentric, Cool Old Guy, who even took the time to build a wall-sized amplifier for Marty to use (which unfortunately overloaded) and built a time machine into a De Lorean because he figured that time travellers should "have some style".
Sirius Black, convicted murderer and long-haired madman-looking figure who scared Ron shitless by appearing in their dorm at night wielding a knife, and who was later revealed to be innocent.
Based on the lies told by his relatives, Harry may himself be this to the residents of Privet Drive. As far as they know, he's the vile delinquent who destroys everything and steals from little kids (that's Dudley and his gang) and attends St. Brutus' Secure Center for Incurably Criminal Boys (he goes to Hogwarts).
Severus Snape may also fall under this category in some ways, at least in his youth. The present version could not be said to have a heart of gold, but he does have good intentions, genuinely trying to keep Harry alive throughout the series, albeit for selfish reasons.
In The Blue Castle Barney Snaith is a loner and rumored to a murderer, a bank robber or both. Valancy doesn't believe it, and it turns out Barney is a nice guy who prefers his privacy, and started some of the rumors, so no one would bother him.
In Dan Abnett's Warhammer 40,000Gaunt's Ghosts novel Blood Pact, Kolding. Reclusive and eccentric after a traumatic ordeal — at sixteen, he was in the hospital when Chaos soldiers attacked to kill the wounded and The Medic, his father — he still comes through for Gaunt. Somewhat Zig-Zagged as we see him first from his own POV and know he's not a freak, but Maggs doesn't trust him. The fact that he's an albino living in the xenophobic mutant-purging Imperium of Man doesn't help either.
In The Lord of the Rings, the people of Bree perceive Aragorn as dangerous—to the point the Butterbur feels the need to warn Frodo against him—simply because he's not a townsman and doesn't fit their understanding of normal. In reality, Aragorn's protection of the town is the primary reason it remains the happy, safe place the townspeople take for granted.
Gives Light: Rafael is hulking, mean looking, and the son of a serial killer. None of the kids on his reservation want to be friends with him, and the boys in his class pick fights with him. But he's as softhearted as they come and has secretly been leaving memorials at the graves of his dad's victims. He also becomes the self-appointed protector of one of the victims' kids. Whom he falls in love with.
Uncle Hoole in Galaxy of Fear is a softer version. Before the books start he adopts the orphaned Tash and Zak Arranda because of his people's views on the orphaned children of family members; he's not of the same species as them, but his brother married their aunt, and since there's no one closer left he has to take them in. Hoole is not a very good guardian. He starts the series as cold and distant, calm during emergencies but snapping peevishly at the children and not wanting to tell them anything. Not even his full name, what he does, where he keeps disappearing to. He's shown to care about the kids, but beyond that this trope is zigzagged and teased at until it's revealed that he is The Atoner.
Harry Dresden is tall, reclusive and bookish. Vanilla mortals think he's a crazy, delusional and fraudulent arsonist. Magical folk and people in the know think he's a crazy, power-mad, psychopathic pyromaniac who destroys anything and anyone who crosses his path. His friends and people who take the time to get to know him may realise that he's just this really nice but socially awkward (and to Thomas' surprise, shy when it comes to romance) guy who is childish and eccentric with a unique sense of humour and a tendency to bite off more than he can chew trying to help those who can't help themselves.
Nico is shown to be very kind, despite all of this, Such as Noticing Hestia when others ignore her, being a real friend to Bob the Titan, and caring deeply fro his half sister Hazel.
On Modern Family, Phil and Claire's neighbor Walt is this. Phil and Claire are terrified of him, but Walt and Luke become very good friends.
Completely subverted on The Golden Girls, a neighbor of the Girls, Frieda Claxton is said to be nasty by Sophia and Blanche, but Rose believes she is just lonely. The Girls are trying to get a tree on Frieda's property saved, and Rose seems to get Frieda on their side, but she shows up at court, and fights for the tree to be destroyed, and only did this to get at Rose.
John Locke from LOST, at least during the first series. Despite no-one knowing much about him and even fewer people trusting him, he nonetheless takes the time to scout for water and hunt for food for the rest of the survivors, as well as form an Odd Friendship with Charlie after helping him through withdrawal, as well as an Intergenerational Friendship with Walt by teaching him survival skills.
Ted Sprague from Heroes. Despite looking like the Unabomber and initially suspected of being the serial killer "Sylar", he's actually just a Nice Guy stuck in one long Trauma Conga Line. Unlike many of the other characters, his nuclear-based abilities don't turn off and are initially tied to his anger, making him effectively a Walking Wasteland that's constantly on the edge of a Super Power Meltdown. Coupled with the guilt of tragically causing his wife to die from severe radiation poisoning and with various people trying to shoot him, it takes a while for people to treat him as more than just a walking timebomb.
Michael Jackson's hero "Maestro" in Ghosts, a 38-minute video. When one of the young boys he was secretly sharing ghost stories and magic tricks with lets the grown-ups in his town know what they were up to, they panic and form a Torches and Pitchforks mob to storm his creepy mansion. The cold-hearted mayor even points out that he lives all alone and is a "freak". Maestro turns out to be a spirit who has a whole troupe of ghosts/ghouls backing him up, and in the end all but the mayor of the town comes to love him thanks to his wonderful powers. Unfortunately, he forces the crowd to witness those powers and tortures the mayor, so the intended "don't be suspicious of/prejudiced towards those who are different" Aesop is muddled thanks to Protagonist-Centered Morality. The story's Reality Subtext — this was after the first round of child molestation allegations against Jackson — doesn't help.
Not really that mysterious as she's a major recurring character but Alice Margatroid seems to fit the other criteria. Perfectly if you replace evil with creepy. Even though she's a Youkai it's debatable that she is leagues more kinder then some of the other "human" characters (Perhaps the kindest in the entire series). If you're ever lost in the Forest of Magic late at night she'll be so kind as to allow you to lodge in her house. As her house is full of dolls and she never makes any kind of conversation, just carrying on with her work without any acknowledgement of your presence one might be a little creeped out.
Subterranean Animism has the heroines on a mission to the Underworld, where youkai were banished that even the surface youkai didn't like. One of these is Satori, mistress of the Palace of the Earth Spirits, whom even the other youkai in the Underworld don't like... because her mind-reading powers and lack of discretion about them unnerve people. She's actually very sweet and mature, and is extremely gracious to you, considering you just broke into her home and beat upher cat.
Time Hollow: Kori Twelves says something seemingly sinister during your first encounter with her, as well as generally acting mysterious, only later on you find she is the victim, not the villain.
Detective Kanski in Secret Files: Tunguska seems like a bad person, telling Nina not to come to her father's office, and threatened them too. Turns out that he is a member of the alien cult (one of the good guys if you don't know), and Nina's "savior", Oleg, is The Mole.
Shirakawa Ritsu in Suika is a lot less disturbing than the initial appearance would suggest.
Igor from the Persona games looks evil, not helped by the molesty vibes people get from him (and further not helped by his summoning you into the Velvet Room in your dreams) and his long, pianist fingers, but he is a really nice guy and is your Spirit Advisor.
Persona 4 gives us Naoto Shirogane, a Kid Detective who is initially standoffish, a bit antisocial and is the dangerous combination of 'working with the Inaba Police' and 'Genre Savvy enough to suspect that your group is hiding important facts crucial to the solving of the case.' When an irritated Rise initially accuses Naoto of treating the case like a game, Naoto doesn't outright deny it, either until just before Naoto puts The Plan to find your secret out into motion. Naoto gets intentionally captured by the kidnapper. You then rescue Naoto from the TV and find out 1) that she was a girl passing herself off as a boy out of insecurity spawned from being a young girl in a profession composed largely of men, 2) as a young girl she didn't have many friends so she immersed herself in detective novels and studying, 3) that she was right about the real murderer/kidnapper not being in jail. After this, she's very open to getting to know the group, though she can still be a touch standoffish and nervous, she immediately offers to help Teddie to find any information about his true identity, despite not even knowing him very well. She makes doctor's appointments for your whole group to make sure that the TV world hasn't physically damaged anybody's health and offers to help Kanji with his math. In summation, Naoto puts on a standoffish hard-boiled facade, but is a helpful all-around sweetheart, dedicated to solving the murders.
Principal Raizo Imawano from Rival Schools, who looks so Obviously Evil it isn't even funny. While he is initially a villain, it's due to being brainwashed rather than any actual evil. And while he did have aspirations to control Japan, he wanted to do so through peaceful methods, such as training his students for political careers (he gives up this goal by the end).
Inverted in Fallout 3. Upon reaching Tenpenny Tower (an upscale luxury gated community) the player overhears a ghoul (zombie-looking heavily irradiated person) arguing about not being allowed to live inside. The ghouls just want to be treated fairly, like human beings, and it's not hidden that the reason they aren't allowed in is because the owner and many of the residents are racist against ghouls. If the layer takes up the owner's quest to descend into the subway tunnels and exterminate the ghouls, they are rewarded negative karma. If you go the other way and find a way to let the ghouls get revenge on the humans' bigotry, the ghouls show up, kill everyone, and wreck the building, and you get really negative karma. If the player goes through the trouble of talking to all the residents, evicting all the racists, and having the others admit they would give coexistence with the ghouls a shot, it seems to work out...for a few days. Unfortunately, a "disagreement" results in all the humans being killed. Still, you tried, so you get positive karma for this solution.
Pokémon Mystery Dungeon: Explorers of Sky gives us Armaldo, a scary looking monster living in a dark forest. Really a Nice Guy and helps our Igglybuff realize his potential as an explorer. Then it's double-subverted; he's a criminal hiding from the police and spread rumors of the monster in order to keep everyone away. It doesn't mean that he's evil but that he has to face up for what he's done. He promises to go exploring again once he's done his time.
A milder example in Mass Effect, Liara T'Soni is an asocial loner more comfortable working with the ruins of dead civilizations than other people, but she turns out to be just shy and is really quite nice.
By the second game she seems to have grown out of it, working as an information broker (and fairly public figure) with her own network of contacts and hired muscle. Then as of the Shadow Broker DLC she's right back to operating from the shadows.
Reclusive neurobiologist Dr. Styles in the adventure game Gray Matter, who is rumored to be a Mad Scientist, and whose solitariness, brusque manner and disfigured face cause him to be feared by most of the people in the surrounding area, but who in actuality is merely a lonely, grief-stricken man mourning the death of his wife.
For part of TV Tome Adventures, whenever The Hero and The Rivalattempt to fight, a silent, absurdly powerful character with the user name "Giga" appears to attack them. He turns out to be an agent for a fictional branch of the FBI, who mistakenly believed that Alpha and Zetto had virus powers which could destabilise the Internet and/or kill all the players of the MMORPG.
Principal Prickly, one of the main antagonists, sometimes appears in this light. Despite having shown to detest the children and appearing to be quite fond of simply locking them up in detention, several times he's shown to really enjoy Recess as an act of nostalgia. One episode even implies that he and several friends hid a chest full of toys from when he was growing up specifically for later students to find. The Movie also sheds further light on this.
Ms. Finster, the other primary antagonist, and Randall fit this trope sometimes with how Randall is sometimes friendly, while Muriel has actually got a heart of gold underneath the hard exterior. The episode where she takes care of Spinelli for the weekend also illustrates this.
Subverted with Mrs. Gerkin on Jimmy Two-Shoes. The end of her first appearance makes her appear to be this, with Jimmy admitting that he misjudged her. The final moments, however, show that she's just as evil as he suspected.
Horrifically subverted in Avatar: The Last Airbender with Hama. Sokka suspects that she's not just an old hermit living alone and until the end, it appears that he's been proven wrong. Then she shows her true colors forcing Katara to learn bloodbending, the ultimate form of waterbending, and cemented herself as one of the most frightening and loathsome characters in the series despite her sympathetic backstory.
Subverted in Family Guy where Peter finds a very old winning ticket allowing him to spend the day with OJ Simpson, who is treated by everyone as being a psychopath. Eventually after showing much generosity he wins the town over.... ending the episode by stabbing several people and making his escape.
Played straight in another episode where Brian meets with an old lady who is a shut in and is forced to take care of her as a part of his sentence. The old woman is extremely bitter and nothing Brian does ever pleases her. It gets to the point where Brian says she should just drop dead and he leaves. When Brian discovers that the old lady used to be a famous opera singer, he feels guilty about what he said to her and he returns back to her home, managing to catch her just in time before she could hang herself. Once Brian tells the woman he liked her aria, she warms up to Brian and becomes a lot nicer to him, happy that someone finally appreciated her classical singing instead of her commercial jingles. Once the woman gets the courage to go outside her house again after so long, she promptly gets run over by a truck and dies shortly after.
My Little Pony: Friendship Is Magic has one episode where the entire town goes into terrified hiding whenever the mysterious cloaked stranger Zecora arrives. Ponies are afraid of her because she looks odd, talks odd, and lives alone in the spooky, mysterious Everfree Forest (where the "plants and animals care for themselves!") Even after Twilight points out that she's a zebra not a pony, everyone is still disturbed; they then blame Zecora for their being cursed, think she's planning to eat them in stew, and so on... In the end they all go off to find her, to get her to remove the curse and "rescue" Applebloom whom they believe has been kidnapped by her. Of course it turns out Zecora had nothing to do with their curse-like maladies and was in fact, working on a cure for them. Also, she would probably have interacted with ponies more, except that whenever she went to town the shops would be "mysteriously closed".
In the Fat Albert Halloween Special, the Cosby Kids think Russel and a girl are trapped in an mysterious old lady's house on Halloween Night. The kids finally get the nerve to burst into the house, but find their friends relaxing in comfortable chairs enjoying some treats supplied by the old lady who, apart from disapproving a bit of the other kids' abrupt entrance, has more for everyone and a merry time is had by all.
Mr. Nebbercracker in Monster House. Part of this is intentional: he deliberately scares kids away so the house doesn't eat them.