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.
Crosses the Line Twice: James' parents abruptly gets eaten by a rhinoceros at the beginning of the story. While having your parents die at a young age is never pleasant, the situation is so absurd, part of you can't help but laugh a little.
The undead pirate scene, which is lead by Jack Skellington, has an expy of Donald Duck among his crew. Six years later, Kingdom Hearts was released, with Donald as one of the main characters and Halloween Town being a playable world, with Jack serving as it's Guest Star Party Member. Likewise, the main party become undead there, though Donald is turned into a Mummy instead.
Ho Yay: A private violin performance of Bach's Partita No. 3, Gavotte en Rondeau, as their mode of transport soars over a moonlit sea seems to edge on the romantic side of things; especially when one considers how flustered Mr. Grasshopper is to be caught by James in the middle of things.
Moral Event Horizon: Both Aunt Sponge and Aunt Spiker are abusive legal guardians towards James in the movie, but they finally crossed it when they outright attempt to MURDER him with axes.
The Woobie: James. Poor, poor James. He had such Good Parents, until they died and his evil aunts took him in. You can guess how well THAT went for him.
Worse, while watching his aunts publicize the giant peach, kids are present there. However, James is forbidden to leave the house, and he sheds a tear as the only possible friends he would make just come and go.
Miss Spider can also come across as this in the book. It's hard not to feel bad for her when she confesses that she doesn't understand why people hate spiders, or when she starts crying while talking about how her relatives were killed in front of her.