Well, perhaps the Scooby Doo gang could time - travel to the era when Jurassic Park was being built. They start to notice strange things happening, like the dinosaurs seem to be more intelligent than they should be. It turns out that a disgruntled employee is using some kind of new technology to control the dinosaurs and make them cause trouble. The gang has to work together, with Scooby and Shaggy providing some comical relief as they are chased by T - rexes and Velma and Fred solving the mystery.
It could be a mad scientist. He might be someone who was fired from Jurassic Park for unethical experiments. So, he decides to take revenge by causing chaos in the park. He uses his scientific knowledge to manipulate the dinosaurs and make them act aggressively towards the Scooby Doo gang and other park visitors.
In a fanfiction crossover, Ghost Rider could end up in the Mystery Machine by accident. His flaming skull would surely freak out the gang. However, he might need their help to track down a villain who has escaped into the world that Scooby Doo and his friends inhabit. They could combine their skills, with Ghost Rider's supernatural powers and the gang's mystery - solving abilities.
One common theme is the clash of different worlds. The Scooby Doo gang is used to more 'family - friendly' mysteries, while Supernatural deals with darker and more dangerous supernatural elements. So when they cross over, there's often a theme of the Scooby gang having to adapt to this new level of danger.
One interesting aspect is the character interactions. For example, when Scooby Doo and his gang cross over with characters from other shows, we get to see how their personalities clash or complement each other. It can be really funny to see the cowardly Scooby interact with a very brave character from another series.
Well, it could be that the Naruto gang gets transported to the Scooby Doo world. Maybe they team up to solve a mystery that involves some sort of ninja - like villain in the Scooby Doo town. Naruto could use his shadow clone jutsu to help search for clues while Scooby and Shaggy are off running from the 'ghost' that's really the bad guy in disguise.
There could be a great story where the Scooby Doo gang is investigating a haunted mansion, which is actually a portal to a darker dimension. Ghost Rider shows up because he senses the evil from that dimension. The gang at first is scared of him, but then they see how he battles the demons that start coming out of the portal. They decide to join forces. Daphne might be intrigued by Ghost Rider's power and try to learn more about it. Fred could use his trap - making skills to help Ghost Rider in combat. Velma could try to figure out the science behind Ghost Rider's powers and how they can use it to close the portal.
One creative storyline could be that the Winchester brothers get stuck in a town haunted by a ghost. The Scooby Doo gang shows up to solve the mystery. Sam and Dean initially think the gang is just a bunch of amateurs, but they soon realize that the gang's skills in unmasking fake ghosts could be useful in their real - life hunting. Another idea is that a demon has possessed one of the Scooby Doo characters, and the Winchesters have to figure out which one and exorcise the demon without scaring the rest of the gang too much. A third could be that there's a cross - dimensional rift that pulls the two groups together to stop an ancient evil that is using both the Supernatural and Scooby Doo universes as its playground.
There's also 'Scooby Doo Meets the Justice League'. In this fanfiction, the Scooby gang stumbles upon a case that requires the help of the Justice League. It's really cool to see how the laid - back Scooby gang interacts with the powerful superheroes. They each bring their own skills to the table, and it makes for a really fun read.
Scooby would probably be really curious about the ponies. He might sniff around them and try to figure out if they were some kind of strange dog - like creatures. Shaggy would be friendly right away, especially if the ponies offered him some food. The ponies, like Pinkie Pie, would be very excited to meet these new and strange visitors. She might throw a big party for them.