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.
Adult Fear: Let's see. There's the confrontation with that grave digger, the time the main trio got locked in that condemned barn, the incident with the new kid falling in with a local thief and nearly dragging Joe along for the ride, the incidents involving David in the mystery books mentioned below under Nightmare Fuel...Wow; even in the 90s, PBS was kinda scary.
Genius Bonus: The contrast between military captain Miles Standish and his intellectual best friend John Alden is a big point in The Courtship of Miles Standish. The episode doesn't really go into that but their counterparts are the modern teenage equivalents: Joe the basketball star and David the science whiz.
The mystery chapter books do it too. One features David disappearing without a trace for at least a day and another features the story's villain trying to run him over for trying to clear his own name. Why is it always David?
Frankenstein (given that they follow the theme of the book, it's pretty hard not to be one).
The scene in Dances with Dogs as Joe remembers his father pushing him on the tire swing is a bit heart wrenching.
The end of the Tale Of Two Cities episode. They keep the "it is a far, far better thing that I do, than I have ever done" line and the guy playing Sydney Carton is actually a pretty good actor. Just try not to think too hard about how he expects no one to notice that a dog has been replaced by a human man.
Joan of Arc saying goodbye to her friend before her execution.