It's nearly impossible to hear "Please Wake Up," a ballad for a dying child, without crying. Michael Crawford himself couldn't get through his first few takes.
To clarify; At the beginning Edgar is so excited that he runs off without kissing his mom goodbye. That's what he remembers when she and the others vanish. Edgar is even seen crying with his friends. Fortunately, it become a heartwarming moment when they’re reunited.
The scene where Edgar gets caught in a man-made trap. It's heartbreaking enough to see him crawling around, blind, calling out desperately for his friends, but then he gets caught and starts crying out of fear. Thankfully, Man is not entirely evil in this film, and the men who do show up let Edgar out of the trap. Though everything leading up to that is pretty intense and sad.
The end of the movie where nearly all of the families are reunited. Though Cornelius has to tell Michelle that though he can't ever replace her mother and father, he'll do his best to raise her.