The caveman who emerges from the Quantum Untangler is an homage/reference to Captain Caveman. He is also voiced by Brent Rose, the actor portraying Fred, meaning Captain Caveman, in this iteration, is a multiversal version of Fred.
Each character has at least one moment of using their famous catchphrase. Velma says, "Jinkies." Shaggy says, "Zoinks!". Daphne says, "Jeepers." White Fred does not traditionally have a catchphrase he does say, "Come on!" three times in the film, demonstrating his classic leadership skills. He also drives the van, another of his standard traits.
While not stated in the film, the writers gave each of the teams variations on the classic Mystery Incorporated name. The prime gang is, of course, Mystery Inc. Then, there is Mystic Inc (the magic users), Mystery X (the paramilitary gang), Mystery Club (the kids), Mystery Busters (the ghost hunters), and finally Mystery Tech (the Terminator riff).
Deacon Carlswell was the manager of a bank in Crystal Cover and better known as The Creeper, a recurring antagonist in the Scooby-Doo franchise. He first appeared in The Legend of Alice May (2010), the sixth episode of the first season of Scooby-Doo! Mystery Incorporated.