A purple flame that must be extinguished to prevent undead from rising. Used this in 4E game for my sons where there was an infinite supply of undead minions (any damage kills them for the non-4E-ers) who kept coming until the flame was found and extinguished.
A ghost trapped in her crypt who must drain the life of some number of sentient creatures before gaining the strength to become corporeal, mortal, able to leave her tomb, etc.
A thief's guild or other such entity that uses fake ghosts and such to deter folks from its lair in the cemetery.
A vault opened by solving a puzzle written across multiple tomb stones. A simple such puzzle could be a combination lock whose combination is the day of the month for the all people who died in the same month and year. There could be other puzzles involving names (the middle initial of everyone with same first letters of the first and last names, first names of everyone with a last name that is the name of a tree, etc.)
A noble undead who, while forced to exist as a loathsome ghoul, wight, etc., seeks to protect the local area from some harm in the cemetery. This is always fun because most players have a hard time thinking of ghouls or the like as anything but absolute evil worthy only of destruction. (They destroy the undead and the thing he was protecting is released. Or they release him from his horrible burden and now have the obligation of taking his place, etc.)
The cemetery is the entry point into a place where the dead live again. Maybe it's a true, heavenly afterlife, maybe its a place that seems at first glance a pleasant afterlife but instead is some horrible, hellish, half-existence where one of the dead holds the others in thrall.
