A ghost town was a settlement in severe disrepair that had been all but deserted, to the point where it seemed to be inhabited by ghosts rather than living individuals.
In 2151, upon seeing the Terra Nova colony close up from Enterprise NX-01's bridge, Trip Tucker thought it looked like a ghost town. (ENT: "Terra Nova")
In 2287, Leonard McCoy blasted Starfleet for sending the bridge crew out on a severely understaffed USS Enterprise-A, calling the ship a virtual ghost town. (Star Trek V: The Final Frontier)
In 2369, newly-installed commanding officer of Deep Space 9 Benjamin Sisko pleaded with Quark not to abandon the Promenade, as he feared if Quark left, others would follow and the Promenade would become a ghost town in short order. (DS9: "Emissary")
In 2399, Doctor Agnes Jurati referred to the Division of Advanced Synthetic Research at the Daystrom Institute as a ghost town, owing to its virtual shutdown after the Attack on Mars. (PIC: "Remembrance")