The Grand High Witch's appearance is horrifying, in all versions. Also, the book invites the young readers or listeners to consider that their teacher — who could be reading the book to them — could be a Witch. It also points out that nice ladies are more likely than nasty ones to be Witches, because they depend on deceit.
The various anecdotes about how children are disposed of by the witches, such as trapping them inside paintings or polymorphing them.
The Grand High's Witch's plan to murder all the children in England.
The transformation scene of Bruno turning into a rat is pretty frightening in itself in the movie version (so much so that most of the scene had to be cut to get a PG rating in the United Kingdom).
When the protagonist is caught by the witches. Throughout the scene, he managed to stay hidden and the reader is lured into a feeling of security that he might just get away. Then, suddenly, one witch catches a whiff of him and the rest of the group turns the room upside-down until they catch him. From there, you know it's just a matter of time until something horrible is done to the poor kid.