* When the gang encounters the Virus in the basement, in the spur of the moment, Daphne can't think of a better insult for it than calling it a [[BuffySpeak Creepy Thingy]]. Not long after that, Fred playfully calls it a thingy, and Daphne gives him the DeathGlare; 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 purple jacket to get its attention, then shouts "Toro! Toro!" At this, the lion stops running and visually has a WhereWhere 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 two Scoobies already get to stealing the fries the Shaggys have.
* The GilliganCut that occurs during the Prehistoric level:
-->'''Fred:''' Where there's a will, there's... ''(They are riding mammoths to the volcano.)''\\
'''Shaggy:''' WOOLLY MAMMOTHS!?
* Scooby and his cyber double doing a MirrorRoutine upon their first encounter.
* The Velmas losing their glasses in the wax museum, and upon finding them, they almost put on each other’s.
* The Scoobys spinning Jaguaro really fast on the merry-go-round, culminating with sending him flying into the milk bottle toss booth.
* The trick mirrors in the haunted house that Daphne and Cyber Daphne encounter. Apparently the latter is just so freaked out by her fat reflection it causes.
** And after trapping the Creeper, Cyber Daphne is at the thin reflecting mirror preening herself, before the real Daphne pulls her away.
* Scooby imitating Officer Wembley. He eventually gets caught.
* The “psychology experiment” scene is probably hilarious; Shaggy asks the Phantom Virus a question, but he only gives him one second to answer, prompting Scooby to shock him with a machine.