- The film was released shortly after Jim Henson's death. Seeing his name in the opening credits caused more than a few tears.
- The stories of the five children who disappeared because of witches. One girl just disappeared without a trace. One boy disappeared after walking off with a woman wearing white gloves. Another boy got turned into a stone statue and his parents used him as an umbrella stand. Another girl got turned into a chicken who laid brown eggs. Another boy got turned into a porpoise after jumping into a river, although he seemed happy with his altered state. But the most tragic story of all is the girl who became trapped in the painting of a farm house her family bought. The most peculiar thing was that she would always change positions in the painting: one day, she would be feeding the ducks, the next day she would be looking out the window and the day after that she would be standing by the fence looking out the painting. And as the years went by, the girl aged as well until she became an old woman and slowly began to vanish until one day she was gone entirely.
- Our hero's parents dying and the grandmother and his reactions after the revelation of this fact in the movie.
- The book's Bittersweet Ending. The Boy is sadly fated to remain a mouse for the rest of his life, and since a mouse-person's lifespan usually lasts about nine years, it's implied he will pass way around the same time as Grandmama (if she's lucky enough to live for another decade). However, he doesn't let this bother him, as long as he gets to spend the rest of his shortened life by his grandma's side.
- The movie's ending, while drastically different, still manages to briefly touch on the situation. As Luke innocently talks about how he'll remain a mouse forever, all Helga can do is silently cry herself to sleep knowing that she may lose her grandson one day. Fortunately, Miss Irvine soon arrives to set things right, restoring the boy's human form and allowing the two to live on like normal.
- Shortly after being transformed into a mouse in Bagieu's novel, The Boy sees his own pet mice and attempts to explain what happened but they no longer recognize him and run away. Hurt by this, he stops to cry.
Tear Jerker / The Witches