The Boo Brothers, Freako, Shreako and Meako, are obviously based on the Three Stooges.
The chest Shaggy opens while searching in the attic is The Chest of Demons (minus the demon face lockplate) from The 13 Ghosts of Scooby-Doo series.
Shaggy's "truck" is actually a Suzuki Samurai.
When Shaggy, Scooby and Scrappy pass through the secret passage that leads them to wine cellar and they get trapped behind it, Freako appears in front of them, using his scary face. Now, in that scene he's not recognized by anyone, but in the next scene you find out that it's him, because he's wearing his hat (while in the previous scene, he was not wearing ii).
Shaggy's Uncle Beauregard is implied to have been a Confederate Colonel. This is not possible, because the film is most likely set in 1987 (the same year it was released in), and if Uncle Beauregard had died around 1987, he would have been at least 140 years old (assuming he was commissioned at 20 years old on the last day of the Civil War).
The family feud between the Beauregards and the Scroggins is an allusion and reference to the Hatfield-McCoy feud.