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.
Comics
Sabrina the Teenage Witch spent at least one story dealing with a hostile haunted house, within which her magical powers were unavailable.
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 a Xanatos Gambit 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.
Somewhat inverted in 13 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.
Really, every town seems to have at least one of these.
Literature
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 moove 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 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, that 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.
House of Leaves: A postmodern horror story about a family that slowly discovers that their house is larger on the inside than on the outside. Much, much larger. Also, possibly there's a monster.
Nick Arcade: The Creepyville board has a haunted house crawling with ghosts that scare Mikey (the player).
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.
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.
While we are on the subject of Stephen King, we can count the Overlook Hotel from The Shining, and Black House.
Liz: Word of advice: If the will says you have to spend the night in a haunted house you better hope that everybody else there is black guys and sluts.
In 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 room mate (that Cordy called 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".
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."
Luigis Mansion is basically 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.
The Elder Scrolls IV: Oblivion has a quest which involves buying a haunted house and clearing it of ghosts.
And there's the titular Atari 2600 game Haunted House and its late-released sequel, which makes it Older Than the NES.
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. Basically, 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 the second No More Heroes game, 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. This is not to mention, of course, the fact that the manor happens to be owned by a vampyre...
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 literally 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.
Western Animation
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 a 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 pretty much 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.
