This is the show that started the tendency to regard Daphne and her family as extremely rich.
This also started the trend of Mystery Inc. being from Coolsville.
Broken Base: To this day, it remains disputed among fans over whether this continuity was a good show in its own right or an inferior Spin-Off Babies adaptation.
Designated Villain: Parodied with Red Herring, who is always at the top of Fred's list of suspects for no good reason. Yes, he's The Bully, but you can't say Fred is being much better with his constant unjustified accusations.
Ensemble Dark Horse: Red remains one of the most memorable characters in the series.
Fan-Preferred Couple: Fred and Red seems rather popular in some circles instead of Fred and Daphne.
Foe Yay Shipping: There are a few circles that ship Fred and Red.
"Scooby Dude" was created to show why Drugs Are Bad. Years later, Carl Steven, Fred's voice actor, became a drug addict before he was found dead from a heroin overdose in 2011.
Fred's parents are not seen in this show, unlike the rest of the gang's. This means nothing if you've seen the direct-to-video movie Scooby Doo! Pirates Ahoy! (where Fred's parents made an appearance and were shown to love and care for their son like good parents should), but Scooby-Doo! Mystery Incorporated and Be Cool, Scooby-Doo! take the absence of Fred's father/parents to depressing levels: they're villains that also run around in monster costumes... or worse.
Daphne being the one who tends to offer Shaggy and Scooby Scooby Snacks, when the Be Cool, Scooby-Doo! episode "Sorcerer Snack Scare" has her objecting to Fred convincing Shaggy and Scooby into risking their necks by offering them Sorcerer Snacks because she sees it as a form of bribery.
"Dawn of the Spooky Shuttle Scuttle Scare" features a character named Mr. Sinclair... not to be confused with ANOTHER Mr. Sinclair.
"Terror Thy Name Is Zombo" has Fred believing in a cotton candy monster from the National Exaggerator. Come Scooby-Doo: Monsters Unleashed, there really was one.
Ho Yay: Fred and Red. Scooby-Doo! Mystery Incorporated has made a few jokes about it by having some incidentals resemble Red during funny moments involving Fred. In one example, Fred is wrestling with a Red-lookalike at a college frat. When the gang finds them in a spooning-like position, he then mentions that they're going to teach him the "happy tapioca", which according to the Urban Dictionary, is a sex position.
Jerkass Woobie: Red Herring, although he's clearly a jerk and bully to the gang, it's hard to not feel bad for him constantly being accused of crimes he did not commit. Though to be fair he has dressed up as a monster on at least four different occasions
Just Here for Godzilla: Even when the mysteries and humor lose some of their appeal, the Awesome Music provides a reason to keep revisiting the show (or at least clips of it).
Strawman Has a Point: Fred accusing Red Herring in "The Computer Walks Among Us" is founded since Velma's robot embarrassed Red Herring at the contest by spraying him with a hose. Given Red Herring's Jerkass personality, it wouldn't be a stretch that he would want revenge.
At the end of "The Schnook Who Took My Comic Book", the gang confronts Mr. Cashmore (one of the suspects who was ultimately proven innocent) about why he was hiding comic books in his car despite him claiming early on in the episode that he hated them. Mr. Cashmore confesses that he actually loves comic books, but is ashamed to admit it because he's a grown man. Rather than make fun of him for being into comic books despite being an adult as was common in the '80s and '90s, the gang assures him that adults reading comic books is no big deal, with their friend, Selma (also an adult), freely admitting that she still reads comic books too.
Carol Colossal was a very successful businesswoman who was portrayed as Ambiguously Brown, a white secretary was shown working under her and clearly outclassed her white male competitors.