John Hejduk published a book in 1985 entitled "Mask of Medusa", an object featured in The Stoney Glare Stare.
After being spooked by the ghost, Shaggy says "Exit, stage left!" This was a catchphrase of Snagglepuss, another Hanna Barbera hero.
Rosey Crans and Gilly Stern are named after Rosencrantz and Guildenstern, two comic relief characters who appear in William Shakespeare's Hamlet. Yorick is named for a posthumous character in the same play (traditionally represented as a skull which Hamlet holds and studies. All three characters appear to have been created by Shakespeare from whole cloth, rather than being taken from an earlier version of the Danish legend.
Mystery Inc. talk about the ghost of Hamlet, then Yorick corrects them and says it is the ghost of Hamlet's father. Technically both are true, as William Shakespeare's play states that Hamlet's father was also named Hamlet.