Not-So-Abandoned Building

Abandoned buildings are something we automatically learn to ignore, which makes them the perfect cover for someone who doesn't want to draw attention to themselves. Like certain less-than-legal businesses, or the Masquerade. Which means that that abandoned building off in the distance, might not be so abandoned after all, it's just kept looking that way to keep out the curious.

Not usually for fight scenes like its close relative Abandoned Warehouse, generally people want to keep this building intact. Doesn't mean there won't be an underground fight club there though.

Film

 * The abandoned lot in the The Shadow turns out to be an entire hotel (the bad guys base) disguised by illusion power.
 * It's revealed in The World Is Not Enough that MI 6 holds some operations out of an abandoned train station, and from what appears to be a wrecked warship in Die Another Day.
 * A half-sunken ship serves as a base in The Man With the Golden Gun.
 * In Following, the burglar Cobb has a few hideouts in abandoned buildings where he stashes stolen goods before fencing them. He notes that London is full of spaces like these, waiting to be used.

Literature

 * In Harry Potter it is noted that, to the perspective of Muggles, Hogwarts looks like an abandoned castle.
 * The Shrieking Shack actually was abandoned, but this made it a convenient place for the Marauders to hang out during Remus Lupin's recurring nights as a werewolf. Dumbledore specifically encouraged rumors about it being haunted to keep curious people from exploring it.
 * Academ's Fury has some of the students go into a decrepit school building... only to open a secret door and take a tunnel into their dojo, where they are learning to be Cursors.
 * In John Sladek's satirical short story "Masterson and the Clerks" the eponymous characters work in what seems like a thriving office building, until a demolition company arrives to tear it down, claiming that it's been abandoned for years.
 * Raylene from Cherie Priest's Chesire Red series is a cat burglar owns a seemingly abandoned warehouse to store things she's stolen. She lets two homeless siblings with prepaid phones to stay there and act as an alarm system, because while an actual security guard or electronic alarm system might look suspicious, homeless squatters in an abandoned warehouse doesn't seem out of the ordinary.
 * In Robert Westall's The Machine Gunners, the gang of children build their secret fortress in the garden of a house that's been destroyed by a bomb blast and deliberately spread false rumours about seeing ghostly lights and other spooky things there to help keep people away. Later, they put up fake War Office signs warning of unexploded bombs and minefields.

Live action tv

 * From Warehouse 13, the eponymous Secret Government Warehouse appears to be nothing more than a run-down building out in the middle of nowhere, when it is in fact a large underground complex.

Video Games

 * The dilapidated planetarium in the aptly-named online puzzle-story Planetarium is ignored by the townspeople and seems to be abandoned, and the story's narrator even points out that the mathemagician's purchase of it is a curious one, considering that he doesn't even visit it all that often. It, of course, turns out to have more than one surprise and living thing hiding in it.

Webcomics

 * Avalons from Skin Deep are where the local monsters go to hang out with each other in their non-human forms; some of them do have members (in human form) stationed around the entrances to keep the everyday Muggles out.

Other

 * It may be a stretch; but would this car commercial count? (In this case it's a car not a building, obviously.)

Real Life

 * Drug labs can sometimes involve abandoned buildings, especially those that produce a great deal of waste.
 * And of course, there's plenty of cases where homeless people will be squatting in abandoned houses.
 * Often perfectly good buildings are kept deliberately abandoned by their owners as an investment, hoping the prices to rise before selling or renting them out. Since this usually requires housing shortage to happen, the practice is often criticized, and regularly activists openly take over these buildings as publicity stunts to make public aware of this wasted space.