Following his disastrous first encounter with Bane, Bruce Wayne created numerous "satellite caves"; a network of bolt-holes and command posts, throughout Gotham where he could go to at a moment's notice to rest and restock. These caves came in handy during Gotham's No Man's Land when the primary cave under Wayne Manor had been decimated by the Cataclysm earthquake. The entrances to this safehouses are usually marked by a bat symbol that can only be seen in infrared.
Batgirl possesses a cave located beneath Gotham that acts as her base of operations. She also had one beneath Bludhaven before the city's destruction.