One sequence in Part Three of JoJo's Bizarre Adventure had the main characters boarding an apparently derelict steamer, with the only passenger being an orangutan. The steamer was actually the orangutan's Stand, Strength. The ape was extremely intelligent by lesser-primate standards and not too fond of people.
One Piece has Thriller Bark, which is basically a floating Haunted House that serves as the base for Gecko Moria and his flunkies. It's mostly filled with zombies, but one of Gecko's crew, Perona, has ghost-like powers granted by the Horo-Horo Fruit.
The ship they found Brook on might be a straighter example: it's a normal, but very old and deserted ship. Except for the walking skeleton. Who promptly gets an invite to Luffy's crew. He accepts.
The Warhammer 40000 spin-off Space Hulk (and the computer game derived from it) is based entirely on the subject of heavily-armed Space Marines boarding a Ghost Ship filled with ugly aliens, in this case Tyranid Genestealers.
Space Hulks are also an important part of 40k's background fluff. These ghost ships are conglomerations of lost and destroyed spaceships and other space debris, which drift randomly through both real- and Warp-space and tend to be full of horrors, of which Chaos worshippers, Orks and Genestealers are the most common and least terrible.
There are also more typical ghost ships, the result of what happens when a ship's Gellar field breaks in the Warp. What happens to the unfortunate crew is best not contemplated, for when such vessels reappear in realspace they tend to either be deserted or filled with daemons instead of men.
There's a whole Chapter made of these, called the Legion of the Damned, who got lost in the Warp and became Warp-Ghosts. When the forces of the Imperium are in dire need, they are said to appear to turn the tide of battle.
Any tabletop game which allows for both undead and ships is likely to feature one of these at least occasionally. In these cases it's not always a mystery how the ship has gone so long without foundering or running aground ... just because there's no living crew doesn't mean there's no crew at all.
Pandorum starts this way but the main characters quickly find out that the ship is filled with murderous creatures with a taste for human flesh. Of course, they're not the worst that's on the ship.
The 2006 made-for-ITV movie Ghost Boat centres on a ghost submarine, which surfaces in the middle of the Black Sea forty years after being reported lost in action, In Working Order but completely empty. It is put back to sea with a crew of modern-day Royal Navy submariners, with the only survivor (played by David Jason) of the original crew on board as well. They retrace the ship's original course as closely as possible, whilst the sole survivor starts to regain his memories of the last few weeks before the boat was lost and he was found floating in his life jacket with a bad concussion. Then things start getting weird... The crew start seeing ghostly German warships and aircraft, and entries in the ship's logbook start appearing where there'd previously been none. The crew start to act increasingly like the WW 2 crew, and eventually David Jason's character has to sabotage the sub when the actions of the possessed captain threaten to start WW 3. The sub sinks with the captain and David Jason aboard... and later is found drifting again, this time looking as battered as a sub abandoned for 40 years should, and with no sign of the bodies of the captain or Jason.
Starship Troopers Invasion Two Mobile Infantry squads are dispatched to investigate the disappearance of the John A. Warden, only to find it adrift with the crew dead... but no bugs to be found. Once power is restored to the ship, the bugs come out of hiding and swarm.
The Dean Koontz novel Phantoms, about a town whose entire population has disappeared or been killed.
In William King's Warhammer 40000 novel Space Wolf, the new marines are sent with a sergeant to find out what happened to another company. They find a tunnel, head down it, and find fragments of Marines' armor. Among other things.
In Ragnor's Claw, they face a space hulk, which is a conglomeration of dead ships, and float in and out of warp without visible control.
At one point Ciaphas Cain reminisces, if that's the term, about boarding a space hulk during his time with the Reclaimers Space Marine chapter. It was infested with purestrain Tyranid genestealers, who proceeded to carve their way through the Space Marines' Terminator armor — the biggest, baddest powered armor a living Marine can wear — without any real trouble.
The seventh novel The Emperor's Finest depicts this period in detail at last.
"Three Skeleton Key", a short story by George G. Toudouze, is about a derelict ship filled with rats running aground and invading a lighthouse. It was famously adapted as an episode of the '50s radio series Escape, narrated by Vincent Price.
In Bram Stoker's Dracula, the Demeter runs aground at Whitby with all the crew missing except the captain, whose corpse is found lashed to the helm. However, a ship's log is found which provides clues as to what happened aboard the vessel.
In several of The History Of The Galaxy novels, characters find derelict ships that have long been abandoned by the crew. In most cases, these are colony ships from the Great Exodus period of human history, when hundreds of these left Earth using an untested and unreliable method of Faster-than-Light Travel.
In one novel, a military officer from Earth is sent by his superior to find the location of the Alpha, the first extrasolar colony ship that disappeared minutes after engaging its engines. He manages to find the ship drifting through a nebula with not a soul aboard. He then gets attacked by a strange cyborg-like creature. Based on the captain's log, he finds out that the colonists were forced to make planetfall on an inhospitable world nearby, leaving the ship adrift in the nebula to gather hydrogen using its Bussard collectors. The cyborg is from a classified military project of that time.
Another novel has the Confederacy of Suns find a derelict planet. Unfortunately, despite being nearly a billion years old, the automated defenses are still functional.
When Septimus and his friends climb aboard the Cerys in Syren, at first it looks deserted - it turns out that pirates have imprisoned the entire crew in a safe room below deck.
The central mystery of the Alex Benedict novel Polaris revolves around a spaceship that abruptly went out of communication and was later found completely empty. All the shuttles and spacesuits were still aboard, the airlocks were still sealed, and the computer had no record of what happened.
Robert Westall short story anthology Break Of Dark features a ghost plane. It returns from a bombing raid intact but with no one alive except the pilot, who's unresponsive and continues to go through the motions of flying it, even after he's been hospitalized.
Several times in Red Dwarf, such as the ship with the DNA-editing machine.
Arguably, Red Dwarf itself may be considered a ghost ship - especially with the distress-signal format of Holly's Opening Narration in early seasons, the demise of the rest of the crew and the tendency of creatures to be lurking in the ship itself.
Space Oddity by David Bowie. It's about, err... an early stage of the orbital derelicthood.
In Star Ruler, ships that lose power from generator destruction, run out of fuel, or suffer crew death (or in the case of a computer controlled ship, power loss) will go derelict and drift off into deep space. Derelict ships can be reclaimed, so long as the equipment needed to run it is still in working shape.
Grandia features a deserted ship with a heavily "undead" atmosphere, although the characters find out that the Big Bad of the ship is just a 'regular' (giant, magic-wielding) squid. This is actually truer to the trope as described here, since they discover what got the crew, rather than undead versions of the crew themselves.
A Homeworld mission had you investigate a ghost ship. While it ignored strike craft, it would immediately take over any capital ship that got within range. When you had no ships in range of its effect, it looked like a derelict in a mass of other derelicts. As an extra bonus, amongst those other derelicts was a missile destroyer - which was extremely effective at taking out strike craft.
In Stationfall, the cause of the station's emptiness turns out to be an alien artifact that corrupts and controls technology; if you lose, it duplicates itself and spreads the copies throughout human space.
Rogue Galaxy had a ghost ship level, which was also the Bonus Dungeon in that particular game, available only after the main story. It even had a special guest NPC.
Suitably for games mostly set at sea, The Legend of Zelda: The Wind Waker and Suikoden IV had Ghost Ship levels. A notable difference is that the player had to chase these ships down on the open sea by following clues, rather than happen upon them by chance as part of the story.
In The Legend of Zelda: Ocarina of Time, Link gets aboard on the fabled "ferry to the other world" in the Shadow Temple, tripulated by Stalfos. Made creepier by the fact that it doesn't sail on water, but on air, and it sinks when it meets the goal line.
The Sandship in Skyward Sword is not haunted, but evokes the feel of a ghost ship because of its derelict appearance and absence of any souls aboard, except for a couple of bats and a miniboss. Once he's defeated, the ship can be reverted to an earlier state via a time displacement field, bringing the crew and the monsters back to life.
The U.S.G. Ishimura of Dead Space is essentially one huge Ghost Ship.
The entrance to the Valley of Bowser in Super Mario World was protected by a ghost ship, that appeared deserted at first, but then suddenly the room fills up with ghosts. It's all but stated, at least in the manual, that it may well be one of the flying ships used by Bowser's minions in Super Mario Bros 3.
Final Fantasy VIII: Squall and Rinoa end up on a spaceship that was abandoned for 17 years and overrun by regenerating alien monsters. Since it is Final Fantasy VIII, the ship is in full working condition, and they clear it of alien monsters and claim it their own with relative ease.
Early on in Final Fantasy V, your party ship is set adrift and end up in a ship graveyard. Naturally, you have to navigate through several derelict ships to reach land, fighting several undead enemies along the way.
Seiken Densetsu 3 at one point in the game has you boarding a ship to get to the next continent. Strangly, no fee is charged (unlike every other boat ride) and when you go to sleep, you wake up to find the ship is actually a ghost ship.
Cryostasis is made of this. A lone meteorologist finds himself on a derelict Soviet nuclear icebreaker, missing for over a decade. The ship is completely frozen, and the crew are either dead and perfectly preserved by the cold, or dead and somehow mutated into ice monsters. The player character also sees both ghosts and flashbacks of events as everything was going to hell aboard.
In Xenogears, the heroes explore a drifting ship whose crew was attacked and killed by the seemingly undead monsters called Wels. At one point, when they turn on the showers and a spray of red fluid pours out, prompting one of them to react with a horrified "what happened on this ship?" - but then it turns out that it's just rusty water.
Mass Effect has one. The MVS Estevanico, which crashed on a planet about a hundred years ago. Even though it's a historical relic, it's falling apart and it's also extremely creepy.
In Mass Effect 2, we have the dead Reaper. Abandoned for what's estimated to be 37 million years, and the people who found it quickly went crazy due to being indoctrinated. The level also counts as an almost literal ghost ship, since even though the ship is all but dead, dead gods still dream.
The Legend of Dragoon has the Queen Fury crashing into a phantom ship filled with undead enemies, and where some important information about the Black Monster is learned.
The "Sunken Ship" level in Okami, complete with Chest Monsters, ghosts that keep floating towards you even on the brush screen, the phantom heads of previous bosses that fly straight into the camera in an apparent attempt to eat your face, Spikes of Doom, a completely inexplicable giant hand that tries to squash you, and a couple of crab-demons living on a pile of bones that turn into an enormous armored shark.
Returns in Okamiden... sort of. You travel to the past just before it gets attacked. You have no idea when this will happen, only that it will. Possibly even scarier this time around, despite not fitting the trope.
Space Griffon VF9. See above example with Space Hulk. Imagine if a Tyranid Tyrant manifested into an ever-evolving monster by not only understanding but controlling and absorbing energy from The Warp, enough to inflict long-distance mind control and mutation upon your fellow soldiers, and change the Genestealers to rogue machines and Body Horror Silent Hill creations. There's a reason why you'll brick the toilet with this game despite the fact it places you in a vaguely familiar transforming mecha. Though, a good half of it IS atmosphere. If you aren't really 'feeling' it, it just won't affect you as much aside from the long-range powers thing.
Mario and company have to explore one of these in Super Mario RPG to retrieve the Star Piece that landed in the ocean. What's unusual about this example is that you actually find out what caused the ship to sink in the first place, and you also get to fight the monster that caused it.
Subverted then played straight in Chrono Cross. The party while sailing through dense fog runs across a ship that is known as a ghost ship and decides to rest, but quickly finds that it's in fact a pirate ship using the legend as a deterrent. After being taken prisoner the party finds out that another ship has arrived directly adjacent, an actual ghost ship... with actual ghosts.
Then, there's the Ravager, which, while not really a ghost ship, it's got the look of one, and it's crew is pretty much made up of zombies, with an actual ghost/Humanoid Abomination for a captain.
The Starship Titanic, due to a premature launch (basically had its moorings cut while the crew finishing out the interior was on break), is populated solely by the robot support staff and an obnoxious parrot belonging to one of the decorators. Oh, and a flock of starlings in one of the upper chambers.
Castlevania Rondo Of Blood and its remake feature a stage set in and around a ghost ship. Worth noting is the painting that comes to life and flies around the room - if it touches you, you're dead! There's also one in Aria Of Sorrow, which is mostly scenery.
Sonic Rush Adventure has the Haunted Ship stage, culminating in a boss battle against a robotic pirate.
Sword of the Stars has the aptly named Alien Derelicts, which are actually broken-off sections of a larger craft. Bear in mind that even so they still are larger than player-buildable dreadnoughts... and their weapons are still active.
Endless Ocean has a large derelict pirate ship which transports the player to and from Ship's Rest, an area with a giant sunken ship that is "haunted" by a very large and pissed off shark.
Halfway through The Adventures Of Rad Gravity, your spaceship is damaged in an asteroid field, and to find spare parts you must search an abandoned ship.
Captain Kunkka in Defense of the Ancients: All-Stars summons a ghost ship that sails across the ground, leaving a trail of rum that protects allies from damage, then crashes and stuns enemies. In the words of his DotA 2 incarnation: "Now that was a failboat".
The first action level of Marathon: RED has you investigate a Pfhor ghost ship, which turns out to be infested by The Virus.
Schlock Mercenary has the Post Dated Check Loan, an old superdestroyer that Tagon's Toughs bought cheap. Turns out that the reason it was so cheap was because it was haunted, and the screams of damned souls- I mean, completely normal plumbing noises, had driven the AI insane. They don't have to fight any monsters or ghosts, and they manage to get the AI and ship into working order relatively swiftly.
In Danny Phantom, all the adults of Amity Park suddenly "disappear", going on a mysterious cruise, leaving all the kids to party and The Hero left pondering the mystery behind it. It's caused by a pirate ghost, complete with a literal Ghost Ship.
The Mary Celeste was found adrift near the Strait of Gibraltar in 1872. The ten people (eight crew and two passengers) who had been aboard when the ship sailed were never found.
While wild theories as to why are still tossed around, a recent book has suggested that fumes from the barrels of industrial alcohol in the ship's hold started to overcome the crew as they were becalmed. To escape the fumes, everyone got into the dinghy to wait for the wind to pick up and blow away the fumes, and somehow the rope came undone. Especially sad because the two passengers were the captain's wife and child.
Another, more plausible theory was given at the time by an experienced sea captain (who had even commanded the Mary Celeste a few years earlier) once he'd checked the weather records and the ship's manifest. The barrels the alcohol was stored in were notorious for losing up to 10% of their contents by evaporation on the run she was on. Normally, the cargo hatches were left open to allow this to be ventilated out, but the weather was bad on most of that run and so the hatches were sealed. When opened during a patch of good weather, enough alcohol vapor could have been present to cause a worrying rumbling sound as it vented off. Knowing how potentially dangerous fire and explosion with such a cargo was, the ship's company might have gotten in the ship's boat and stood off at the end of a line to wait for things to calm down (or blow up). In this instance, they would have taken the ship's papers, charts, and navigational instruments with them in case the ship did blow up, and these were all missing from the ship when it was found. If the weather turned too rough to return to the ship, they would have had no choice but to wait and hope it got better. Apparently, it didn't, and the line parted under the rising stress of the bad weather and rough seas.
Quite a few real life examples can be found on the list here.
Scurvy or epidemic diseases have been known to wipe out all hands.
In 2007, the catamaran Kaz II was found deserted with the engines running and all the lifejackets still on board. Like the Mary Celeste, the three crew members were never found.
In another instance, according to an urban myth, a few teenagers rented a pleasure yacht, sailed out into the open sea, and all jumped into water for a swim - but forgot to loosen a ladder to climb back on board. As a result, they all ended up drowning as they couldn't mount the boat's slick walls from the water. Naturally, the boat was found before the teenagers.