In Keroro Gunsou, the Hinata house is haunted by a Cute Ghost Girl who appears sporadically throughout the series. She turns out to be really a very nice person. Also, she kinda sucks at haunting.
Ghost Hunt had one, based on the Winchester Mystery House.
One chapter of Digimon V Tamer features Taichi, Zero and Gabou going to a haunted house to find one of the V-Tags.
0012 in Cyborg 009 may be the consciousness of a human cybernetically transferred to a mansion, but for all intents and purposes, this mansion is a haunted house: She can project her voice and a holographic image anywhere in the house; make objects levitate and manipulate the walls, floors, and ceilings; and has placed the house in a dark forest when 009 and the others arrive.
Comics
Sabrina the Teenage Witch spent at least one story dealing with a hostile haunted house, within which her magical powers were unavailable.
Dr. Brainstorm attempts to scare Calvin and co. with one in "The Great Halloween Heist".
Socrates' mansion (which has a rather gruesome backstory) is believed to be one in "Pranking the Ghosts".
The gang comes upon another one in "Dark Laughter".
Film
The little cabin in The Evil Dead contains a haunted book, so, for all intents and purposes, is haunted.
Gracey Manor in The Haunted Mansion (2003) starring Eddie Murphy is a parody.
Beetlejuice is a haunted house comedy from the perspective of the ghosts.
Darkness (2002), starring Anna Paquin, had a family moving into a haunted house as part of an Evil Plan to complete a demonic ritual.
Poltergeist features a suburban California home that is normal at first, but is invaded by ghosts that torment the owners in various ways. Because it was built on top of a cemetery.
Invoked in Thir13en Ghosts in which an occultist builds an infernal engine in the form of a glass house, then deliberately moves ghosts into it as a power source.
The Haunting in Connecticut: The house was formerly a funeral home.
The Burbs: The suburban house next door takes on some cliches of a haunted house after the extraordinarily creepy neighbors move in. Though it's not haunted, the neighbors do turn out to be a clan of murderers.
The Changeling from 1980 features George C. Scott moving into a house that is haunted by the ghost of a crippled child who was drowned in the bathtub by his father.
Played straight and Inverted in The Others starring Nicole Kidman. The house is haunted, but by the main characters, who don't realize that they're dead.
The Grudge Haunted By Kayako, her son Toshio, and Toshio's cat.
Literature
Judith Spearing's Ghosts Who Went to School had a house filled with a ghost family. The bank who owned the property couldn't sell it, despite it being well maintained by the resident ghosts.
Shirley Jackson's classic novel, The Haunting Of Hill House. The first paragraph has been cited by Stephen King as one of the finest openings in English-language literature:
No live organism can continue for long to exist sanely under conditions of absolute reality; even larks and katydids are supposed, by some, to dream. Hill House, not sane, stood by itself against its hills, holding darkness within; it had stood so for eighty years and might stand for eighty more. Within, walls continued upright, bricks met neatly, floors were firm, and doors were sensibly shut; silence lay steadily against the wood and stone of Hill House, and whatever walked there, walked alone.
Matheson's Hell House rivals Shirley Jackson's Hill House.
In Myth Adventures Skeeve received from the natives (Deveels), notoriously canny businessmen, a big house on Deva as a part of a deal. Why do they give him a cheap house? It has a back door that leads to the Uberwald-like vampire dimension.
And the native vampires avoid it as haunted. Some even say they saw humans there — just imagine it!
The Shrieking Shack in the Harry Potter series. Arguably, Sirius Black's house as well.
The Shrieking Shack wasn't really haunted, but people thought it was due to the strange noises coming from it (which were caused by Lupin in his werewolf phase).
Technically the Weasley's house had a ghoul in the attic.
Subverted in Tom's Midnight Garden. Tom only thinks he is staying in a haunted house; in truth, he is travelling through time, during which he is able to pass through solid objects and people.
Subverted in The Haunting of Grade Three, where the eponymous third-grade class has relocated to an old house, which has mysterious noises and objects that move seemingly of their own accord. In truth, the house is sinking, which accounts for the odd noises and movements.
Subverted in The Ghosts of Cougar Island, which features an abandoned, seemingly haunted house. In truth, the "haunting" is caused by some runaway orphans.
In "The Shunned House" by H. P. Lovecraft, the hero of the story becomes obsessed with a mysterious house that, since it was first built, wound up either driving its occupants insane or causing them a slow wasting death. It turned out that the house was built over the final resting place of a magician who slowly drained the Life Force from the people near him in the night.
Also the titular house in "The Dreams in the Witch-House" has a haunted reputation, but is actually periodically visited by a living, immortal witch who used to live in the house, and still uses its sealed attic for her work.
Arabian Nights: The story Ali the Cairene and the Haunted House in Baghdad.
Edbrook Manor from Haunted 1988 is haunted by ghosts.
Anne Rivers Siddons' The House Next Door is a very strange example in that the house is still unbuilt at the start of the book, and there's no obvious reason why it turns out the way it does (it's not built on a cemetery, for example). All the same, it's a very Bad Place indeed. It's the architect that's cursed. All his previous projects were unfinished because someone died or was blinded in a freak construction incident. No reason why it's him but he was adopted and doesn't know who his real parents were, so that tells us something. After they kill him and are killed by the house someone finds the plans to that house and it looks like it's going to happen again.
The Clancy House, in Vampires Don't Wear Polka Dots, where Mrs. Jeepers moves in. This is what initially signals to the kids that Mrs. Jeepers is a vampire.
In The Dark Tower series, the Dean brothers visit the reputedly-haunted Mansion, but never work up the nerve to go inside. This was a wise decision, as the house itself is the guardian of a portal between worlds. A very aggressive guardian.
We can also count the Overlook Hotel from The Shining, and Black House.
Subverted in Chris Bohjalian's The Night Strangers. There are bones in the basement and multiple ghosts wandering around. However, the bones belong to a child who isn't haunting the house, and the ghosts are attached to the protagonist, ex-pilot Chip Linton, not to the house itself.
In the first season of American Horror Story, the house is haunted by numerous previous residents who died there. Anyone who dies on the premises appears to become a ghost, and this leads to something of a snowballing effect when the ghosts start killing people.
In Being Human, George and Mitchell are able to rent a city centre house on the cheap because it's haunted by a girl called Annie. George, being a werewolf, and Mitchell, being a vampire, don't have a problem with this.
The haunted, gothic Collinwood Mansion is featured in Dark Shadows.
The British domestic comedySo Haunt Me deals with a suburban home haunted by its previous resident, a Jewish Mother. While the father is mostly annoyed by her presence, the other family members generally enjoy her company.
Buffy the Vampire Slayer had a couple of these in its time, such as in "Fear Itself" and "Where the Wild Things Are".
Cordelia's apartment in Angel was also haunted. Except the ghost was friendly and generally treated like an invisible roommate (that Cordy called 'The Phantom Dennis').
That's because she found out his name while doing research for the place. Mainly because it was originally haunted by Dennis' mother who was far less nice, and attempted to kill Cordelia or convince her to commit suicide, believing her to be Dennis' fiance, who she hated in life.
And the reason behind the said haunting was that Dennis's mother walled him in a closet to keep him from moving out to live with the said fiance, and suffered a heart attack immediately afterwards.
In the The Sarah Jane Adventures episode "The Eternity Trap", Sarah Jane, Rani and Clyde accompany Professor Rivers to investigate Ashen Hill Manor, supposedly one of the most haunted houses in Britain. As Clyde puts it, it's "Hogwarts, Tim Burton-style".
Aaargh Manor is reputed to be the most haunted house in Bottom World, in The Legend Of Dick And Dom. The owner is faking it... but there is actually a ghost there as well.
The X-Files, episode "How the Ghosts Stole Christmas". Mulder and Scully visit one on Christmas Eve to find the ghosts of two star-crossed lovers who formed a Suicide Pact.
Scully: Mulder, tell me you didn't call me out here on Christmas Eve to go ghost busting with you.
Mulder: Technically speaking, they're called apparitions.
Doctor Who - "Blink" was described by Russell T Davies as the revival's first proper "haunted house" story (except with creepy alien statues instead of ghosts). "Hide" has a haunted house that no-one will go near except the local investigator, who, to Clara's bewilderment, went to the trouble of buying it.
Music
Diana Thornton's "Lover's Last Chance". The song starts by describing innocent childhood Halloween fun, but then< "All of them hush past the house on the corner/A darkened old mansion than never did sell/Even the grownups just whisper about her/Nobody knows how she died... or won't tell."
The titular "Loa House" in King Diamond's song by the same title, from the Voodoo album.
Genesis' 1983 song "Home by the Sea" is the tale of a robber who breaks into a house only to find that it's haunted.
"The 13th Hour" (album) by Midnight Syndicate. The album's premise is the exploration of a haunted Victorian mansion once inhabited by the Haverghast family.
Run For Your Lives is an annual event. Runners go through a 5 mile obstacle course in the wilderness which is infested with zombies.
The Haunted House dark ride at Alton Towers. Later got a much Lighter and Softer update and became Duel, where you shoot lasers at the monsters and spirits in the haunted house.
Final Fantasy VII has a Haunted House as the hotel at the Gold Saucer amusement park. The receptionist drops down from the gallows whenever you check in.
Luigis Mansion is the story of Mario's hapless younger brother getting a free house... which he then has to clear of ghosts. Apparently, the whole thing was a ghostly creation, and it disappears when he's done. For some reason, the money in it wasn't, so he buys a new one. Which is presumably not haunted.
In Luigi's Mansion: Dark Moon, E. Gadd lives in one, albeit one inhabited by much more friendly ghosts than normal, due to the influence of the Dark Moon. When the Moon breaks, the ghosts are driven to mischief and malice and he is forced out.
The House point-and-click Flash game series focuses on exploring a house whose inhabitants committed suicide. Or did they?
Unsurprisingly, used in The Lost Crown: A Ghosthunting Adventure. Also a Haunted Museum, two Haunted Churches, a Haunted Boathouse, etc. If it's got a roof, some ghosts are sheltering under it.
Spookyraven Manor in Kingdom Of Loathing, with such bizzare undead as the "Pooltergeist" (made out of Snooker balls) and "Undead Elbow Macaroni".
While the main threat in the first two Clock Tower games is Scissorman, the Barrow's mansion and Barrow's Castle are both haunted, and have various other threats within them.
The Haunted Mansion for the Gamecube. Playing it as a kid and being used to Mario Kart and other kiddy games did NOT help whenever rotting arms burst out of boarded doors and "The Ring" girl in a red dress flipped her hair up with a screech.
In No More Heroes 2: Desperate Struggle, Travis fights Matt Helms, a ghost kid who haunts his creepy, abandoned house, complete with a graveyard on the front lawn.
The entirety of Sweet Home takes place in one of these, referred to as a "House of Residing Evil."
Draynor Manor in RuneScape. The front doors refuse to open from the inside, the grounds are filled with dead trees (some of which can and will lash out and attack), the eyes in paintings frequently follow the player... As do chairs. The manor happens to be owned by a vampyre...
Shining The Holy Ark has a massive sprawling mansion in the middle of a graveyard where the powerful being Galm lives. The house has seen much better days. Seeing how Galm was only released from imprisonment you do have to wonder who built such a massive house (which is bigger than the King's castle) and why it was abandoned.
Shining Force III had another mansion with yet another Vandal living in it. He had transformed all the village folk into Kyon-Shi. Dantares, the brave Knight, is teased by the young mage about being scared of ghosts at this point in the game.
The Seventh Guest had the protagonist moving about a haunted house built by an evil toy maker.
Tales of Phantasia features Demitel's manor, a dungeon where aside from undead abd monsters in the garden, the only inhabitant is Demitel himself.
Pokémon Black 2 and White 2 has the Strange House. There's a ghost girl in it and the furniture keeps re-arranging when you leave and re-enter the main room and basement. The girl makes a few comments each time you encounter her, alluding to the tragedy that befell her and her family there, and disappears after you get the Lunar Wing from her. Ghost, Psychic, and Dark type Pokemon can be found in it too.
Prior to that, Pokemon Diamond And Pearl had the Old Chateau, which was the first location in the series to have human ghosts wandering around— an old man would sometimes appear in the dining room, and a little girl could appear in the upper level room on the far right if you entered an adjacent room. And, as usual, the place is full of Ghost-types, including the one-per-game Rotom.
Webcomics
In Annyseed, Uncle Tarkwin's mansion is known to be haunted. Perry Elliot, the ghost, frequently visits the library, and, (though he would like you to believe otherwise) Anny's bedroom.
Stupidity in Magic has this. Twice, actually. Both times, the main cast is only called in to see why the house is haunted - they never get the house itself (they have their own place already, anyways). The first time, the ghosts were stuck in the house because of a curse, and most of them were happy to leave once the problem was fixed. The second time, the ghosts were haunting a house being rented out by a college - the rent was very reasonable, due to the haunting, and the college students only called for help because the ghosts had started possessing the occupants and were getting a bit violent; once things were fixed so that they wouldn't be in danger of getting hurt any more and they realized why the rent was so low, they were quite willing to let the ghosts stay - they preferred slightly-haunted accomodations that were within walking distance of the college to anything else they could've afforded.
Olive Specter's home in The Sims 2. Actually, if you have a Sim die on your lot, their ghost will show up and cause trouble.
This is the backbone of Amber: Journeys Beyond.Rule of Three on the ghosts, one from roughly 1910-1920, one from 1942, and a third from the late fifties.
The Global Guardians PBEM Universe: Doctor Ka's New Orleans mansion is home to hundreds of ghosts. And some of them are angry. Very, very angry.
The student republics in the new Forum/RPG, Grave Academy, akin to Hogwart's Houses, all have elements of this, the students being monsters probably help.
The trio of heroes from Filmations Ghostbusters set up shop in what resembled a run-down haunted house—Ghost Command—that featured haunted appliances such as (most memorably) the wisecracking Ansabone. Similarly, the Big Bad Prime Evil had Hauntquarters, a cathedral-like building located in the Fifth Dimension.
In The Simpsons Treehouse of Horror segment, the Simpsons move into a haunted house, which does its best to make them leave... but they refuse, because it's their dream house. The segment ends with the house destroying itself rather than live with the Simpsons.
Lisa: You can't help but feel a little rejected.
Subverted in another episode, where the family have to spend the night in a haunted house. Homer, foolishly, says it's perfectly safe since there's no such thing as ghosts. The spooky music rises and the door slams behind them, complete with a flash of lightning... Next morning, the sun is shining and it's beautiful out, and they've had a pleasant night's sleep and absolutely nothing's happened.
In The Simpsons' sister show Futurama, Bender the robot inherits a castle and finds it's haunted by robot ghosts. The haunting is stopped when they find that it was caused by improperly shielded cables from the robot cemetery. Still it led to this great exchange:
Uncle: Come to us, Bender. You'll like being dead!
Bender: That's what they said about being alive.
Who Killed Who is about a detective trying to find a killer in a spooky house; he encounters ghosts, skeletons, and Santa Claus along the way.
, making it Older Than Feudalism.
Compare Haunted Headquarters, which is any haunted primary setting, and Old Dark House, which may or may not have a supernatural element. Big Boo's Haunt is this trope in video games. Will often end up invoking Never Recycle a Building, for good reason.
If it's merely the setting for a Scooby-Doo Hoax involving Ten Little Murder Victims, see Old Dark House.
For the Atari 2600 game of the same name, go here.
