In the scene where Tom gets angry after digging in the backyard, and kicks the bucket towards the wall, it was not supposed to hit and break the window. This was a "happy accident", and it was used in the film, as Kevin Bacon stayed in character, and continued the scene.
In the hypnotism flashback scene, there is a scene of a safety pin being stuck through Tom's hand. This was not a special effect - a stunt man was paid to come in and have a safety pin pushed through his hand for the scene.
On the couch, the babysitter reads "The Shrinking Man" by Richard Matheson, author of "A Stir of Echoes", the basis for this film.
When they were setting up the scene where Maggie leaves Jake at her relative's house, it was realized that they had gone over the number of hours the child actor that plays Jake could work (due to strict Hollywood child labor laws). Crew members had to run from house to house in the neighborhood they were filming in to find a child who looked enough like him to appear as a background character (after their parents' approval and a very quick hair cut) to be able to complete the shot.
The hypnosis sequence in which Tom (Kevin Bacon) is hypnotized for the first time follows actual hypnosis techniques used by professional hypnotists. In order to ensure that the audience hasn't been put to sleep (and some susceptible people have been), there's a musical accent at the close of the sequence to wake everyone up.