A commonly unacknowledged trope from The New Scooby-Doo Mysteries was that many episodes parodied classic literature and/or pop culture. Not only this, but often little Easter Eggs were included in the episodes, including every minor character being named after characters or elements of the parodied work.
The most prominent examples of this would be in "Scoo-Be or Not Scoo-Be?", in which the gang visits the Castle Hamlet Hotel. Besides the villain being the ghost of Hamlet, every minor character was named after a character from Hamlet, including Rosie Crans (Rosencrantz), Gilly Stern (Guildenstern) and Yorick (Old Man Yorick).
"Sherlock Doo" parodies Sherlock Holmes, but also has this same trope of naming all characters after characters from Sherlock Holmes. These include: Iggy and Ziggy Moriarty (Sherlock's rival Inspector Moriarty), Mr. Lestrade (Inspector Lestrade), Mrs. Adler (Irene Adler), and Mr. Stapleton (Jack and Beryl Stapleton from The Hound of the Baskervilles). 221B Baker Street is the address utilized in this episode, which is in continuity with the Sherlock Holmes franchise.
A Christmas Carol is parodied in "The Nutcracker Scoob," where the gang has to help an old miser wanting to tear down a children's home find the true meaning of Christmas. A performance of The Nutcracker was also thrown in as part of the gang's theatrical performance.
Besides literature, The New Scooby-Doo Mysteries also parodied pop culture. "Happy Birthday, Scooby-Doo!" is essentially an episode-long parody of 'This is Your Life' hosted by Mark Winkendale, who is caricatured in this episode as "Wink Martindale."
"Mission Un-Doo-Able" parodies Mission Impossible with a high-stakes government threat narrative perpetrated by a supervillain, in this case, Mastermind. The "self-destruct" message that was used in this episode was a common trope in the Mission Impossible films of the 1960s.
Other episodes like "The Bee Team," "A Code in the Nose" and "Doom Service" also parody pop culture icons like The A-Team (along with Mr. T as 'Mr. BLT'), Goldfinger, and The Shining, respectively.
Finally, in "Scooby's Peep-Hole Pandemonium," the whole episode is a sort-of parody of a classic monster movie, even parodying Norma Desmond, a creepy actress character from the film Sunset Boulevard made in 1950. Even the journalist, Orson Kane, is a parody of Orson Welles from the film Citizen Kane.
Though The New Scooby-Doo Mysteries isn't exactly the most critically beloved series of Scooby-Doo, it's very interesting to see how much of a pop culture aspect they went for this particular series, especially in the episodes where they named the entire cast of minor characters after the parodied media.