It's common knowledge among the fandom that Supernatural crossed over with Scooby-Doo for the one-hour special Scoobynatural. However, it's lesser known that there are actually tons of Scooby-Doo references throughout the fifteen seasons of Supernatural. In two episodes, "Regarding Dean" and "The Rising Son," the characters are seen watching "Hassle in the Castle" and "That's Snow Ghost," respectively.
There are also a ton of Scooby-Doo references related to Dean, as he's a Scooby-Doo fan in the series. In the season 2 episode "Playthings," Dean mentions "Might even run into Fred and Daphne while we're inside. Mhm, Daphne. Love her." when they go into a haunted house. One character says "This ain't Scooby-Doo" in the season 3 opener "The Magnificent Seven." In season 6's "All Dogs Go to Heaven," Dean asks "where's this little Scooby gang of yours?" In the season 8 episode "The Great Escapist," Dean comments that the hotel manager looks like a Scooby-Doo villain. In "Dog Dean Afternoon" from season 9, Dean exclaims "Ruh-roh!" In "#thinman" from season 9, Dean threatens the villains by saying "You two clowns are gonna get into that Mystery Machine outside, and you're gonna leave town." Season 11's "Form and Void" has Dean commenting "Listen Velma, this isn't the Scooby gang, okay. So either shut up or get out," to which Crowley comments he's "more of a Daphne." Lastly, in the final season, Dean mentions in "Golden Time" that he pulled an all-nighter just to watch Scooby, and in "Last Holiday," Dean is shown to own Scooby-Doo underwear.