Most video games tend to have a Space themed stage as one of the final levels and a city type level is usually one of the first however the movie seems to reverse things.
When the gang encounters the Virus in the basement, Daphne can't think of a better insult for it than calling it a Creepy Thingy. Not long after it, Fred calls it a thingy, and Daphne gives him the Death Glare. Velma finds it funny.
There's something hilarious about Shaggy and Scooby eating the cafeteria dry, and one chase with the Phantom Virus later, they've immediately slimmed down again.
On that note, the montage of their chase is pretty hilarious too, with them releasing the animal test subjects to trample the virus, blowing up the chemistry lab, using a robot to beat him around and finally pushing him into a bookcase.
During the montage across levels 4 and 9, one of the Scooby Snacks is in the arms of a princess chained to a tree and a dragon is about to eat her. Shaggy beats the dragon and saves the princess. The princess is ready to kiss her knight in shining armor...but then Shaggy just goes for the Scooby Snacks and teleports out.
Fred's attempt at using bullfighting techniques on a lion in the Colosseum level - he uses a blue jacket to get its attention, then shouts "Toro! Toro!" At this, the lion stops running and visually has a "Where? Where?" reaction. Fred rolls his eyes and shouts, "Leo! Leo!" It works.
The hilarious reactions of the gang meeting their cyber doubles. Perhaps most hilarious is both Daphnes immediately critiquing each other's fashion.
Also, the 2 Scoobys already get to stealing the fries the Shaggys have.