This initially started as a joke on my part, later dubbed Crack Theory A. It was a commentary about how Shaggy would do things like levitate or pull things out of nowhere. Normally, not even worth a mention in a cartoon. Except he and Scooby are the only ones that do this.
But the more I watched, the more it seemed like less of a joke. Things like Shaggy painting a doorway and having it turn real, or the way the two inflated themselves in ‘The Beasts Awake at the Bottomless Lake’ seemed to take it a bit further.
The first overtly supernatural occurrence in Scooby-Doo as a whole was Shaggy unwittingly casting a spell and its reverse in 'Highrise Hairraiser’ Actual supernaturals can out of the woodwork to show themselves to him, but almost never the rest of the gang. He even got a job in a monster’s only school.
It’s not just the old stuff too. Newer movies still have him being the only one to see supernatural stuff (Samurai Sword) or know it was real (Kiss Rock and Roll Mystery). He also did things like not needing to inhale for 3 hours and lots of acrobatic stunts that shouldn’t have been possible (Legend of the Phantosaur)
The kicker was ‘Scooby-Doo and the Goblin King,’ in which you have a magical character who seems to expect Shaggy to already be familiar with magic and flat out calls him a wizard (once clearly and once inferred).