Given that this is a theatrical movie, there is great deal of nostalgia and callbacks thrown in not just to the Scooby-Doo franchise, but also to several other Hanna-Barbera cartoons:
- The younger Shaggy is first seen outside a fast food stall called Casey's Creations, named after Shaggy's original voice actor, Casey Kasem.
- Alexander's Great Gyros, where Scooby is first seen, is shown to be established in 1969, the year Scooby Doo, Where Are You? premiered.
- A stylized version of Squiddly Diddly appears as a mural on the side of a building when young Scooby evades the police. A more traditional rendering of him appears later in the film on a billboard for Bubbleland.
- Also visible during said chase is "Ruby's Subs", which offers free vegetable "Spears" with every order — a reference to Joe Ruby and Ken Spears, the original show's co-creators.
- Scooby and Shaggy are big fans of Blue Falcon, like in Scooby-Doo! Mask of the Blue Falcon.
- The current Blue Falcon being the son and successor of the original Falcon was a fictional story detail in the Show Within a Show in Mask of...
- Likewise, as a kid Shaggy was a fan of The Impossibles (in their guise as a rock band), and has paraphernalia all over his room. Later, when they're trick or treating, you can see a trio of kids dressed as them as well.
- On Halloween, young Daphne is dressed as Wonder Woman, who had a Blink And You'll Miss It cameo in Mask of the Blue Falcon.
- Silhouettes of Fred and Wilma Flintstone are visible when Young Daphne is cornered by the ghost.
- The opening sequence of Scooby-Doo, Where Are You!, accompanied by its signature theme song, is accurately recreated almost shot-by-shot in CGI animation, although with several changes.
- After the prologue, the Mystery Machine is first shown only from profile, much like it was on the show (as it was easier to draw and they could reuse the animation to save time and costs).
- The group gathers and meets Simon Callow at "R&S Coffee Shop", initials for "Ruby and Spears" again.
- As the Mystery Machine is driving along, you can see Hanna's Barber Shop and Barbera's Pizza; an ad for Pitstop Perfume can be glimpsed when Fred turns the van around.
- Peebles Pet Shop is visible in the first shot with the Mystery Machine.
- Next to it is a bowling alley called Takamoto Bowl, named after longtime Hanna-Barbera producer and the designer of Scooby-Doo himself, Iwao Takamoto. The bowling alley clerk is even credited as Judy Takamoto.
- The Bowling Alley building itself is modeled after the exterior of the original Hanna-Barbera studio building.
- While they're bowling, Scooby-Doo copies Fred Flintstone's signature bowling style for a moment.
- There's graffiti reading "Top Cat" in the alleyway where Scooby and Shaggy are cornered by the robots.
- Dee Dee has patches on her sleeves with a Teen Angels symbol.
- Velma's investigation into Dick Dastardly takes her to a kennel club website; one of the bits of text says they have a new arrival, a light-blue dog named "Huckleberry".
- Billboards for Quest Industries, Jellystone Park, and Cogswell Cogs can be seen during the gang's drive through the country in search for Shaggy and Scooby.
- When Fred decides to take a "shortcut", they pass by Silverman's Service Station, a reference to Fred Silverman, the CBS exec who originally picked up the show.
- When both Scooby and Shaggy hide from Dastardly in an abandoned arcade, a poster of The Hex Girls can be seen along with a poster for The Neptunes when Shaggy and Scooby are on the Wack-A-Mole. They also barricade the door with, among other things, an arcade cabinet with Hong Kong Phooey on the side, along with cabinets titled The Laff-A-Lympians and Space Stars.
- Officer Jaffe is named after Nicole Jaffe, Velma's original voice actress.
- An attractive, blond woman actually being the male villain in a bizarrely convincing disguise recycles an identical gag from Scooby-Doo 2.
- Messick Mountain is named after Scooby and Muttley's original voice actor Don Messick. In addition, Messick's vocals are used for Muttley's snickerings and the Spooky Space Kook's cameo int the intro.
- The second skull is located at Mystery Island. (one of HB's live action segment shows)
- The last skull is referred to by the cavemen as a "Slaghoople", which is Wilma Flintstone's maiden name.
- The inhabitants of Mystery Island resemble the Slag Brothers and one of them uses a turtle like a horn similarly to how animals are used for every day objects in the Flintstones.
- The pterodactyls all resemble Turu from Jonny Quest, except purple-colored, smaller, and mostly harmless.
- In an episode of What's New, Scooby-Doo?, Scooby dressed up as the Greek demon guard dog Cerberus. Guess who he meets in this film?
- Cerberus also appeared as an antagonist on The New Adventures of Huckleberry Finn and was also given an unnatural color to him there, the only difference being this film's was green and Huck Finn's was blue. Both had glowing green eyes and guarded a gate to the underworld located in Greece.
- As racers, Dastardly and Muttley were sponsored by Winchell Motor Oil, a reference to Paul Winchell, Dastardly's original actor.
- Yankee Doodle Pigeon, which Dick Dastardly kept chasing in his Flying Machines cartoon, appears... stuffed and mounted.
- Captain Caveman combines his portrayals from the Flintstones Comedy Show (a newspaper office boy) with the Teen Angels show (teams up with Dee Dee Sykes).
- Simon Cowell appearing as a caricature of himself continues the tradition of celebrity guests appearing in Scooby Doo properties, an idea that first started with The New Scooby-Doo Movies.
- The final scene has the whole gang gather around the laptop in the same pose used at the end of the Scooby Doo, Where Are You credits. Also, the laptop has Quest Industries' symbol, and the gang meets Dr. Quest himself in the post-credits shots. He, along with the rest of the Quest team, and his company has cameo'd in Scooby-Doo! Mystery Incorporated.
- Dick Dastardly's robot goons are called the Rottens. Originally, he was planned to be the team leader for the Really Rottens in the Laff-A-Lympics, but rights to the character meant they went for a Suspiciously Similar Substitute instead.
- Dick Dastardly's airship appears to be designed as a combination of his Mean Machine from Wacky Races and the SS Dirty Tricks from Yogi's Treasure Hunt. The Mean Machine itself appears during the credits.
- "B.O.B." by Outkast is played during the end of the second act. Guess which hip hop duo recorded a song for the 2002 film?
- During the credits, Atom Ant, Jabberjaw, The Great Grape Ape and Captain Caveman are shown to have joined the Falcon Force alongside Blue Falcon, Dee Dee and Dynomutt.
- Like in A Pup Named Scooby-Doo, the gang have been friends since they were pre-teens. What's New, Scooby-Doo? also followed the same suit as revealed in a flashback.
