I just finished The Goblet of Fire for the fourth time, but this time I read it while watching out for "Professor Moody"s behavior during school. One piece that stands out is the Defense Against the Dark Arts lesson where Barty Crouch Jr. shows all of the students the Unforgiveable Curses.
This alone wouldn't be weird, as we know it was important that Barty played the eccentric/paranoid character of Mad-Eye well. However, he makes it a point during the lesson to continue using the Imperius Curse on Harry until Harry can resist it. Ignoring the fact that Harry learned to resist one of the most dangerous curses in the magical world in an hour-long class (Aurors should sign up for that, huh?) - what possible motivation would Barty have to teach/train Harry Potter how to resist a very useful Dark spell? Voldemort, later in the same book, even tries to use the Imperius Curse on Harry and can't (one would assume this is due to the earlier training).
The argument of "fitting in" doesn't seem to apply here, as merely demonstrating the curses at all was already straining the limits of Mad Eye's eccentric reputation; plus he only repeatedly targeted Harry. He could just as easily have not aroused suspicion by showing them the curses, or Imperius-ing all of the students equally. The only thing Barty accomplished was strengthening Harry's chances against Voldemort.
There's also the possibility that he simply hated the boy who defeated his master, and as such, wanted to torture him. But in that case, why not "teach them to resist/experience" the Cruciatus Curse? It has just as flimsy of an excuse (i.e. "showing them how it works") but with far more effective results. Furthermore, making a student jump on top of a desk would hardly qualify as torture, even someone as loony as Barty.