These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Depending on the Artist: Similar to the fluctuation of models and layouts in Looney Tunes depending on the various directors, animation in Where Are You! never consistently stuck to one specific model per episode, and the variety of Hanna-Barbera's animators drawing styles often showed from scene to scene.
Ensemble Darkhorse: The Creeper is, far and away, the most popular and iconic Monster of the Week ever to be featured on this show. Notably, he's one of the few characters on the original show outside of the main Mystery Inc. gang to become a well-remembered character in his own right, and was even popular enough that his daughter became a featured villain in Scooby-Doo! Mystery Incorporated (which aired four decades after the Creeper's only episode).
And then there's the Space Kook, for his Crazy Awesome design and laugh.
Ho Yay Shipping: From "Jeepers, It's the Creeper": At the school's barn dance, Shaggy is dancing with Velma when Scooby enters and asks Shaggy to let him cut in. To Velma's shock and disappointment, Scooby goes off dancing with Shaggy.
Memetic Mutation: "Scooby Snacks", Scooby's manner of speech, "You Meddling Kids", and (after the villain is unmasked) "It was Mr. Jameson, the fairground owner!"
The popular Millennial slang term "creeper" (used to describe someone perceived as threatening or unsavory) may well have originated as a reference to this show's popular Monster of the Week the Creeper.
Moral Event Horizon: Some of the things pulled by the villains of various episodes—the Ghost Clown trying to feed Shaggy to a lion, the Snow Ghost trying to saw Velma in half and then sending dynamite after her and Scooby, the ghost of Captain Cutler locking Fred, Daphne, and Velma in an underwater room, etc. Not to mention the kidnappings that were more prevalent. This gives Shaggy and Scooby a reason for their Lovable Coward moments, because there's an element of real danger despite the ghosts being fake.
Uncanny Valley: In-Universe. One episode that didn't feature a villain in disguise, "Foul Play in Funland", had the heroes help an Inventor capture a runaway robot he built for an amusement park. It turns out the inventor's sister sabotaged the robot to persuade him not to put the robot to use, because it would scare the children away.