Surprisingly not a lot in film, at least from what I can recall, significantly disrupted me emotionally. I do remember being totally enthralled and at times terrified by Jurassic Park, but in a really engaging, positive way. As a child I adored dinosaurs would regularly check out paleontology books from the library for my Mum and Dad to read to me. Jurassic Park was the culmination of all these things put to cinema with such believability that it really dug deep beneath the skin. Raptors in the kitchen was the stuff if awesome nightmares.
Television however far more commonly fucked me up, in particular when I'd cop a sneak peak at an X-Files episode or something like that. I was also obsessed with stories of extraterrestrials, Grey abductions, and other spooky nonsense. To my shame, there's an episode of Lois & Clark: The New Adventures of Superman where the two fall asleep in their car and wake up from a time lapse (classic abduction story), and have incremental flashbacks after the fact of staring up first person from a table as eerily figures loom over with masks and scalpels.
This sequences scared the absolute fucking shit out of me. Probably more than anything.