There are some truly incredible ones in here, so I'm going to list ones that, up to this point, have not been listed. Hopefully I won't be ninja'd.
"You've gotta ask yourself one question: 'Do I feel lucky?' Well, do ya punk?" I know this is seen as more of cool quote than a scary one, but then think if someone was asking YOU that question.
"A boy's best friend is his mother." One of those quotes that has to be in context.
"Listen to them: The children of the night. What sweet music they make." Probably the classiest of the scary quotes.
"The greatest trick the devil ever pulled was convincing the world he didn't exist."
"He let's the last hungarian go. He waits until his wife and kids are in the ground and then he goes after the rest of the mob. He kills their kids. He kills their wives. He kills their parents and their parents' friends. He burns down the houses they live in and the stores they work in. He kills people that owe them money. And like that *blows* he's gone."
"Keaton always said 'I don't believe in God, but I'm afraid of him.' Well I believe in God, and the only thing that scares me is Keyser Söze."
The Usual Suspects is such an incredible movie.
"Please know that we have added a consequence for failure. Any contact with the chamber floor will result in an unsatisfactory mark on your official testing record, followed by death."
"Would you kindly?"
"When Picasso became bored of painting people, he started representing them as cubes and other abstract forms. The world called him a genius! I've spent my entire surgical career creating the same tired shapes, over and over again: the cleft chin, the upturned nose, the ample bosom. Wouldn't it be wonderful if I could do with a knife what that old Spaniard did with a brush?"
"The Wild Bunny by Sander Cohen: I want to take the ears off, but I can't. I hop, and when I hop, I never get off the ground. It's my curse, my eternal curse! I want to take the ears off but I can't! It's my curse! It's my fucking curse! I want to take the ears off! Please! Take them off! Please!"
Bioshock is so damn amazing.
These next three aren't presented as being scary, but out of context they can be. First the character Wyoming from Red vs. Blue
"Looks like it's your lucky day, mate. I don't have time to torture you, so I'm just going to have to kill you."
Next is the end of the Voltaire song "Dead." Once again, presented in a humorous manner, but out of context...
"God is all knowing / And God is all seeing / Just who do you think that you are to change his mind? / He already knows what you want / And decided that you didn't need it / So don't bother asking for cures or an answer / God is the one who gave you the cancer."
Finally we have a bit by the phenomenal George Carlin about "the greatest bullshit story ever told." Being a stand up comic, of course you laugh when he says it, but when you think about it it's a testament to how some people are unwilling to think for themselves.
"Religion has actually convinced people that there's an invisible man living in the sky who watches everything you do, every minute of every day. And the invisible man has a special list of ten things he does not want you to do. And if you any of these ten things he has a special place full of fire and smoke and burning and torture and anguish where he will send you to live and suffer and burn and choke and scream and cry forever and ever, until the end of time. But he loves you."
NOTE PLEASE READ: Just to keep this from turning into a hate war I am not atheist or anti-christian or anti-religious, I just don't believe in blind faith. Take everything with a grain of salt.
Finally, a quote that can't be written. It must be heard. Unfortunately due to all the parody's of this scene on youtube, this is the best I could get.