The adventure genre should probably get the award for best ghost pirate of all time (Monkey Island's LeChuck), but the award for most prolific use of both ghosts and pirates in a genre has to go to RPGs. RPGs were overdoing the pirate thing well before pirates were overdone as a general fad. And any RPG fan knows that it's not a real quest until you've encountered a ghost ship as either a dungeon or a boss. Naturally, these two mainstays overlap from time to time.
To be considered for this illustrious list, each RPG must have:
1) actual ghosts of pirates who reside on a ship which itself may be a ghostly apparition (but not necessarily), or
2) a seafaring vessel that at one point was used by pirates but is now haunted in some fashion, or
3) a seafaring vessel that is currently being used or at the very least being occupied by pirates that is concurrently haunted by ghosts which may or may not be related to the pirates, or
4) an apparitional ship on which earthly pirates reside
5) a ghost ship disguised as a pirate ship or vice versa
To find such ships, one must only go where the fog is, and enter with an open heart.
Above: What what whaaaat?
So, these regular pirates have been disguising themselves as a ghost ship to hide out from bad guy Lynx, which maybe is not the best idea considering how easy it seems to be to stumble upon ghost ships in this genre. So, good luck with that, guys.
Super Mario RPG: Legend of the Seven Stars
Above: Anthropomorphic sharks really do make the best pirates
Greapers are definitely ghostly, but rightly you might be asking yourself if Dry Bones actually counts as a ghost. He's undead to be sure, but we can probably all agree that true ghosts must be incorporeal (except if they like, try hard enough, love someone enough, and/orown a pottery wheel).
Well, the Pure Water item which is used to kill ghosts in the game works on Dry Bones, therefore Dry Bones is a ghost in the world of Super Mario RPG which is all that matters. Case closed.
Rhapsody: A Musical Adventure
Above: Best not to question it
Sadly, many crewmates were lost in the catastrophe, including the beloved Libinsky whose special lady was waiting for him back home. All the crew suspect Libinsky's best friend Tarkoff of letting him drown when he could have rescued him, so Libinsky returns as a ghost to set the record straight and clear his friend's name.
Above: In a recent survey of ghosts, "unfinished business" was the #1 answer for why they've returned