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Needed: History is missing details.
The clubhouse was a treehouse located in Shaggy Rogers's backyard (next to Scooby-Doo's doghouse). The preadolescent gang frequented there to hang out and solve crimes.
A Pup Named Scooby-Doo
At the clubhouse, Shaggy told the gang about his stolen bike.
The gang ran there to hide from a real (but nice) ghost.
The gang met there to discuss things after Velma Dinkley was accused of stealing possessions from Coolsville Junior High School.
Freddie Jones was making wanted posters for Red Herring there when his friends asked him to stop accusing the bully for 24 hours.
Velma demonstrated her teleporter there and then transported them all to New York City.
The gang was attacked by the Ghost of Mrs. Shusham, who wanted Shaggy to return a delayed book.
Hanna-Barbera Presents: A Pup Named Scooby-Doo
Daphne (disguised as a vampire) attacked the rest of the gang at the clubhouse.