Scooby-Doo! Mystery Incorporated manages to pull from a lot of Scooby-Doo media.
- Shaggy and Scooby love watching Vincent Van Ghoul movies and they, along with the rest of the gang, eventually end up meeting him during two separate episodes.
- Velma's parents run a supernatural tour of the city, which references many ghosts from the original series, such as The Miner 49'er. When Velma's forced to work as a tour guide, she takes great pleasure in explaining to the gaping tourists just how fake each and every one of them were.
- The Spanish conquistadors whose ghosts appear repeatedly as the series builds to its conclusion have a lot in common with Morgan Moonscar and his pirates from Scooby-Doo on Zombie Island: both groups had been ruthless pillagers in life, who fell afoul of genuine evil magic and were denied the opportunity to rest in peace in death; both also did their best to warn the Scooby gang of danger and to arrange for the evil they'd contributed to unleashing to ultimately be put to right. Oh, and both played a key Posthumous Character role in groundbreaking Scooby-Doo installments that took the franchise along much darker and more mature paths than ever before.
- A Don Knotts caricature can be seen amongst the tourists in the first episode, and he appears again at the beginning of Episode 9. Knotts famously guest-starred on The New Scooby-Doo Movies.
- Nugget Nose AKA The Galloping Ghost (a very obscure 1978 Hanna-Barbera feature from Yogi's Space Race, an equally obscure show) can be seen during the historical montage about Gatorburg.
- Mama Cass Elliot, another The New Scooby-Doo Movies guest star, is one of the attendees at the auction for a painting. Amazing feat, as she has been dead since 1974.
- In "Secret of the Ghost Rig", while in her bedroom knitting an ascot for Fred, Daphne hums the theme from The New Scooby-Doo Movies.
- The haybaler scene from the 1970 episode Jeepers, It's The Creeper is re-created, save for the baby chick that mistakes Scooby as its mother.
- In "In Fear of the Phantom", the Hex Girls, who first appeared in Scooby-Doo! and the Witch's Ghost, make a reappearance. Not only that, but they sing some of the songs from that movie.
- Likewise, when they reappear in Episode 38, not only are they wearing their original outfits from Scooby-Doo and the Witch's Ghost, but they perform "Who Do Voodoo?", which they sang in their second appearance in Scooby-Doo! and the Legend of the Vampire.
- Also in "In Fear of the Phantom" was Harry the ventriloquist's dummy. Shaggy threw his voice a few times in the classic series.
- In Episode 8, Velma calls Daphne by her old nickname "Danger-prone Daphne" after she falls into the hidden door inside a tree.
- The revelation that the concept of a gang of mystery solvers with a Team Pet spans back for generations, with the Scooby gang being the latest one, could be seen as a nod to a period during Hanna-Barbera's history where the company went wild with Scooby-Mania and made several Scooby-Doo clones like Jabberjaw or The Funky Phantom.
- Like the What's New episode "Large Dragon At Large", Velma bristles at the thought of wearing an Olde English maiden's outfit. Unlike the What's New episode, she doesn't wear one.
- In a web game tie-in, one sidequest has Shaggy and Scooby collecting scattered pages of a play script. Shaggy notes that the play's set in a town called "Coolsville" (from A Pup Named Scooby-Doo and the live-action Scooby-Doo movies) and the main suspect is named Red Herring (also from Pup).
- Suzie Chan, from The Amazing Chan and the Chan Clan, appears in Episodes 6 and 16.
- A poster of her and Stanley can be seen on HP Hatecraft's wall in Episode 25.
- Along with a poster of Prez Rickard, the Teen President of the United States from an obscure 1973 DC Comics series (and later, The Sandman).
- The Monster Museum at the beginning of Episode 20 sees a statue of Flim-Flam (who Daphne described as getting 25-to-life, despite being a pre-teen con artist), and when she sees a statue of Scrappy Doo:Daphne: Wow! I haven't seen—
Fred: Look away, Daphne! We all promised each other that we would never speak of it. Not ever! - Episode 21: Linda Cardellini, Velma from the live-action theatrical movies, is the voice of Hot Dog Water. That makes two members of that cast (the other being Matthew Lillard as Shaggy) giving voices to this animated production.
- The high-tech costume and superweaponry Alice May used in her Oblivia the Obliteratrix disguise were supplied to her by a man on Destroido's payroll: Benton Quest.
- The pose for the yearbook photo of the original Mystery Inc. is similar to a pose that Scooby's Mystery Inc. had in Scooby-Doo, Where Are You!? theme song.
- The current-day Mystery Inc. also strikes that pose at one point.
- Episode 27: Crybaby Clown tells the gang that Mano Tiki Tia (original series ep "A Tiki Scare Is No Fair") and the Ghost of Redbeard ("Go Away Ghost Ship and Ghostly Creep From The Deep") are nothing compared to him.
- Episode 37: The seal named Scooby was seen eating a box of snacks with Scooby written on it. Also, he and his friends are from the Moby Dick segments of the Hanna-Barbera cartoon Moby Dick and Mighty Mightor, and their fathers are from the Hanna-Barbera cartoon Sealab 2020.
- Episode 39: Charlie the Robot from the original Scooby-Doo, Where Are You! cartoon plays a key role in the mystery.
- In "Heart of Evil", there is a Scooby Snacks box on the table. Also, when Scooby and Dynomutt meet, their high-five routine is exactly the same as Scooby and Scooby-Dum in the opening sequence of The Scooby-Doo Show (which was the other half of The Scooby-Doo/Dynomutt Hour).
- The Grand Finale ends with the gang deciding to head out to the other side of the country via roadtrip and solve every mystery they come across along the way. Pretty much a reference to the original series.
- The scene where they are watching the new Mr. E's message, the group are positioned and posed around Velma's laptop in the exact same way as the scene from the first episode (also featured in the theme song) where the gang are researching the magnifying glasses clue (with the book replaced with her laptop).
