Star Wars: Ascendancy: Early in their voyage, the crew of the Chimaera come across a large Celaphid starship floating abandoned within an asteroid field.To make things worse, one of the investigative team happens to be the former first officer of the missing ship. The Enterprise crew, on going to investigate, finds only corpses aboard.
Star Trek: The Original Series fanfic Something Wicked This Way Comes has a missing starship appear out of nowhere a decade after it vanished.Unfortunately, it's not quite vacant it's filled to the brim with hostile Promethean Crawlers. Remnants: The multi-group alliance ends up finding and exploring the wreck of a long-crashed Forerunner cargo ship.Left Behind forces Crichton and Chiana to work on helping the abandoned Leviathan Rohvu recover after they're left behind by the rest of Moya's crew (due to the Moya crew leaving with other versions of Crichton and Chiana on board) at one point Crichton accidentally breaks a piece of Rohvu and Rohvu doesn't notice because he's in so much pain already after two cycles with Kaarvok and the Xarai eating bits of him.This in turn resulted in many Ghost Ship sightings and rumors, one of which nearly started World War III with the abyssified USS America swimming in Russian waters. Eternity: Years before the War started, the Abyssals were testing the waters.Soul Eater has the ghost ship Nidhogg, captained by the Flying Dutchman himself.Queen's Blade Rebellion: Captain Liliana's ship can fly and has an Undead Pirate Crew (herself included despite not looking undead).There's even a flying ghost ship that is said to appear and later shows up having been enthralled by Ainz offscreen. Overlord (2012): The Katze Plains have been a designated battleground for centuries, to the point where undead spawn constantly there.Who promptly gets an invite to Luffy's crew. The ship they found Brook on might be a straighter example: it's a normal, but very old and deserted ship.It's mostly filled with zombies, but one of Gecko's crew, Perona, has ghost-like powers granted by the Horo-Horo Fruit. Thriller Bark, which is basically a floating Haunted House that serves as the base for Gecko Moria and his flunkies.The ape is extremely intelligent by lesser-primate standards and not too fond of people. The steamer is actually the orangutan's Stand, Strength.