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  • The gang from Speed Buggy make a brief cameo at the end of the second episode.
  • This isn't the first time Mark Hamill has teamed up with Mystery Inc As Himself, having done so in a parody of The New Scooby-Doo Movies, Night of the Living Doo.
  • And, of course, Mystery, Inc. has teamed up with the Caped Crusader multiple times, on The New Scooby-Doo Movies, Batman: The Brave and the Bold, and the Direct to Video film Scooby-Doo! & Batman: The Brave and the Bold.
  • Wonder Woman's design is based on her DC Animated Universe design (her physical appearance) with elements of her Justice League Action design (her outfit and shield).
  • Likewise, Batman appears in his DC Animated Universe design, also with elements of his Justice League Action design.
  • The Chris Paul episode features Shaggy playing golf, something he was known for in What's New, Scooby-Doo?.
    • At one point, the gang and Chris Paul go underwater in diving suits very reminiscent of those from episode 2 of Scooby-Doo, Where Are You! .
    • There's a gag where Shaggy and Scooby pretend to run a class and draw an immature picture to upset the monster, much like in the season 1 finale of Be Cool, Scooby-Doo!.
  • In the Funky Phantom's guest star episode, the ghost of Abraham Lincoln turns out to be Mudsy in disguise, which is very similar to The Reveal in Scooby-Doo! Mystery Incorporated episode "Mystery Solvers Club State Finals", an episode featuring guest star appearances from numerous Hanna-Barbera cartoons (including The Funky Phantom) that emulated Scooby-Doo. There is a notable difference, though, since in that episode, Mudsy was actually the villain; he was revealed to not being a real ghost, just an unemployed actor who eventually got sick of the teens always getting all the glory, and masqueraded as the Monster of the Week in order to kidnap the mystery-solving teen teams. He also didn't really exist as the episode was a fever dream of Scooby. Here he is definitely a real ghost, and his intentions are entirely noble — he pretends to be the ghost of Abraham Lincoln in order to give pep talks and get the two competing mystery-solving teens to work together.
  • The shot of Mystery Inc. and the Funky Phantom Crew looking at Shaggy and Scooby in the diner is modeled after the iconic shot of Mystery Inc. looking at the camera from "What a Night for a Knight", famous for being the penultimate shot in the original theme song, right down to Velma seated holding up a book, or in this case, a map.
  • In the episode "Elementary, My Dear Shaggy", one of the sounds the Screaming Skulls of London make is the distictive whooping cackle of the Spooky Space Kook.
  • In the Penn & Teller episode, the gang pass by a painting of the Indian Witch Doctor from the Where Are You? episode "Decoy for a Dognapper".
  • Just a shade over fifty years since the very first episode, "What a Night for a Knight" aired, episode 13 with Batman is titled "What a Night for a Dark Knight!"
  • The "Weird Al" Yankovic episode has a dinosaur as the Monster of the Week, a reference to Weird Al's song "Jurassic Park" (a parody of "MacArthur Park").
  • In episode 11, Shaggy and Scooby eat only vegan food while they're staying at Sia's mansion. In What's New, Scooby-Doo?, Shaggy is portrayed as a vegetarian due to his VA Casey Kasem becoming one. Sia is also a vegan.
  • Also at Sia's mansion, her doppelgänger is seen hanging from a chandelier at one point, a reference to Sia's Signature Song "Chandelier".
  • The Batman episode is a mix of the DC Animated Universe, Justice League Action, and the 1960s TV series. The latter particularly with the music, the Batmobile, and the bust of William Shakespeare.
    • In the same episode, the abandoned department store is called "Miller & Frank", a reference to Frank Miller.
    • Issue 277 of the Batman comics had Alfred have a niece named Daphne, although she was a different character altogether.
    • The scene where Scooby-Doo keeps bouncing through the air and beating on Man-Bat is reminiscent of the Where Are You? episode "Never Ape an Ape Man," when he did the same thing to the titular Monster of the Week.
  • "One Minute Mysteries":
    • The Flash locks up several classic Scooby-Doo monsters in Iron Heights with The Creeper being the only one caught normally.
    • Barry Allen, Shaggy, and Scooby hang out in Big Belly Burger at the beginning of the episode, which is Flash's favorite fast food chain in the comics and various TV shows.
    • At the end of the episode, the mysterious teddy bear bomber is revealed to be The Joker underneath, but Freddy notices it's another mask, revealing The Trickster. Both are played by Mark Hamill in various previous DC works.
  • During the chase sequence in "A Run Cycle Through Time":
    • The gang ride through on a green car, with the group dressed similarly to characters from Wacky Races, most notably Daphne as Penelope Pitstop.
    • Scooby and Shaggy briefly get turned into their child selves which are based off of their designs in A Pup Named Scooby-Doo and SCOOB!
    • The gang rides on a Tyrannosaurus that is colored purple, similar to the one in Scooby-Doo and the Cyber Chase. Moreover, it's not the first purple T-Rex to be popular in media. The clothes the gang wears are also based on the main four outfits of The Flintstones, though with a different color scheme.
    • Same episode, but before the chase, the gang land in the year 4545, ruled by a tyrant Scooby and rebellion leader Shaggy. Scooby's robotic design very closely resembles Dynomutt, while Shaggy's cyborg parts look like, well, Cyborg.
  • "The Hot Dog Dog" has the Haggerty Hotdog mascot, whose Goofy Suit includes a mask that bears an uncanny resemblance to Scooby-Doo, very similar to the Scooby Latex Perfection mask the titular villain wore in the classic episode "Never Ape an Ape Man" for pulling a Mirror Routine on the real Scooby.
  • The plot of "A Moveable Mystery!" is notably similar to the What's New, Scooby-Doo? episode "Ready to Scare". Both episodes take place at a fashion show in Paris (and feature a detour to the Parisian catacombs), and both have very similar monsters (gargoyles who both turn out to be people who are important to running the fashion show.)
  • In "Total Jeopardy", the Gang hide in barrels to avoid being spotted by Max the Robot, with Scooby bumping into Max, popping his head out of the barrel, followed by an ominous closeup of Max's face. This mirrors a scene from "Foul Play in Fun Land", the Where Are You? episode with Charlie the Robot, which was also part of the series' intro.
  • In "When-Urkel Bots Go Bad", the Technomancer's design is almost directly taken from the Green Ghosts from Where Are You's "A Night of Fright is No Delight", just with computer code moving around the robe and lacking the shackles, but when the Gang removes the mask, the costume loses the computer code and better resembles that monster.
  • In "A Fashion Nightmare!", when Tim Gunn tells Shaggy to imagine his wardrobe, all he sees is a closet full of green shirts and brown pants... with the exception of a single red shirt (which he wore in the 80's), which he promptly removes.
  • In "Cher, Scooby, and the Sargasso Sea", Cher mentions encountering another shark monster the first time she met the Scooby gang, a reference to the "Mystery on Shark Island" episode of The New Scooby-Doo Movies.
  • In "Scooby On Ice!" when the village elder complains about the snow games causing a bunch of ruckus and flimflam, Scooby thinks she's talking about Flim-Flam McScam. Shaggy adds how he's helped them with at least 13 ghosts.
  • In "Scooby-Doo and the Sky Town Cool School!", the pterosaur is a brown Palette Swap of Turu the Pteranodon from Jonny Quest.

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