"Okay, now come up with a plan that doesn't involve your ten-year-old sister joining the Army!" Which like the above example happens during a very dramatic scene and probably wasn't meant to be that funny, but it is.
Meta example. While shooting the scene where Ray and the kids are in the water, while the Tripods are plucking civilians one by one, Steven Spielberg and John Williams pulled a prank on Cruise, Fanning, Chatwin and the extras in the water at the time, by playing the theme from Jaws over the loudspeakers.
While driving away from the Tripods Ray tries to explain to Robbie what's attacking everything:
Robbie: What is it? Is it terrorists?
Ray: These came from some place else.
Robbie: What do you mean, like, Europe?
Ray: No, Robbie, not like Europe!
Immediately preceeding this scene, Rachel cries/screams "is it the terrorists?" too, in what may now seem a Hilarious in Hindsight manner.