The Running Gag where Scooby-Doo is being teased by two gophers, may be a reference to Caddyshack, as both this and the episode takes place on a golf course.
Episode 2: "A Mystery-Solving Gang Divided!"
Fred says, "We'll head 'em off at the pass!" to which Daphne replies, "I hate that cliché!
Episode 3: "Peebles' Pet Shop of Terrible Terrors!"
Shaggy is bitten by a bulldog that looks just like Bandit from Jonny Quest.
Magilla Gorilla forming a friendship with the kitten Mr. Jones is a reference to Koko the gorilla.
Episode 7: "The Cursed Cabinet of Professor Madds Markson!"
The scene where The Mystery Gang, Penn and Tess Flemming all escape out of the Savannath Hotel before it burst up in flames is a callback to McClane's escape.
The episode featuring Steve Urkel has him frequently earn the ire of a loud-mouthed, overweight man with a mustache, and having to deal with evil robots. There is even Sonic's "juicing/revving" sound effect heard when Urkel reactivates his robot made in his own image. Steve's voice and inflections are even used for Princess Sonia Hedgehog, Sonic's sister in Sonic Underground. Sound and feel familiar?
The Allosaurus has the same roar as the Tyrannosaurus rex from the films.
Scooby, Shaggy, and Weird Al attempt to hide from the Allosaurus by standing very still, under the assumption it cannot see movement. It doesn't work, though.
The Allosaurus chases after the Mystery Machine, complete with Shaggy urging Fred to go faster and a rear-view mirror shot.
Episode 15: "The Sword, the Fox, and the Scooby-Doo!"
Several to "Star Wars" from Shaggy and Scooby-Doo using fish as Lightsabers to one of the trashcans in the backgrounds looking like R2D2, likely due to the fact that Luke Skywalker is the guest of the day in the episode.
Another one to Star Wars is the various photographs Shaggy keeps having Mark sign. They are all done to look like paintings, just like the classic movie posters for the franchise before Disney acquired it.
The fur pattern on the fox monster is reminiscent of the eponymous creature from My Neighbor Totoro.
The first attempt to capture the fox monster is a reference to the Japanese story of Kiyohime.
The Flash pulling Daphne, Velma, and Fred out of the exploding toy factory at high speed is reminiscent of a similar scene involving rival speedster Quicksilver from X-Men: Apocalypse.
In a reference to a very specific episode of Star Trek: The Original Series, George Takei wields a fencing sabre while shirtless, and mentioning Richelieu.
In a reference to ST:TOS episode, "Return of the Archons", Mystery Inc. first show up cloaked in brown hooded robes.
George Takei tells Fred to drive faster. Fred replies,"She'll shake apart!" George replies, "Shake her apart, then!"
Episode 18: "The New York Underground!"
The Scooby-Dooby Doors scene includes a reference to the Teenage Mutant Ninja Turtles. At some point in this scene, which is set in the sewers, the Gator Man Monster is seen running away from Mystery Inc. and Halsey, who are all wearing red ninja headbands. Scooby, Halsey, Velma, and Fred are wielding a nunchaku, a pair of katana, a pair of sai, and a bō respectively, while Shaggy uses a skateboard and is eating a slice of pizza, all of which are trademarks of the Ninja Turtles.
Episode 19: "Fear of the Fire Beast!"
Scooby and Shaggy (accidentally) end up with a Spaghetti Kiss only to fight over the spaghetti, much like how Santa's Little Helper and his lover She's the Fastest did in The Simpsons episode "Two Dozen and One Greyhounds".
Episode 20: "Too Many Dummies!"
The gang stays at a creepy motel with a mansion in the background that looks suspiciously like the Bates house.
The evil dummy is designed to look like The Joker, and seems to be channeling Paul Lynde for his voice.
Episode 21: "Dance Matron of Mayhem!"
Episode 22: "The Wedding Witch of Wainsly Hall!"
Episode 23: "A Run Cycle Through Time!"
When Scooby-Doo and Shaggy spotted a Giant Banana in the future, they say the following:
Shaggy: Come on, Scoob, I think it's time we went-
When Thorn greets the delivery man, she says, "Welcome to our nightmare," a reference to Alice Cooper.
Thorn's bat necklace was redesigned slightly to resemble the red bat emblem from Batman Beyond.
When trying to stall for time, Scooby Doo goes out on stage and says "Hello, Cleveland!"
Episode 25: "The High School Wolfmans Musical Lament!"
While more of a Take That! than a Shout-Out, during the song "Diners for Dinner, Dinner for Diners". "Christian Slater" says "I love hearing a dog talk, and you know i don't mean Scrappy."