Why are people naming scenes from horrors when the title of the thread is "Scariest Sci-Fi Film Scenes." Things like Blair Witch should not even be mentioned as it is a psychological horror not Sci-fi.
Scariest scenes in Sci-Fi for me are as follows.
Chest busting scene from Alien, something that is hard for most men to watch as it symbolizes giving birth.
Also the scenes in Wrath of Khan with the alien bugs being trapped in the space suits with Checkov and the other Captain, imagine a worm or something crawling into your ear and doing things to your brain.
McPherson tapes scene I must admit is quite a good choice too.