I think quite a few Data moments are pretty scary just because he's generally so nice and logical and wouldn't do anything freaky (like stab Troi. Repeatedly.)
E.g. 'Geordi, what... does it feel like when a person is losing his mind?'
Pn a similar note - Data's head in Time's Arrow I first saw a picture on the internet, in the dark, in bed when I was scrolling through some stuff about Data and I jumped about a metre it really freaked me out.
One of the few moments I have actually screamed while watching TV would be in Sub Rosa when the ghost appears in the mirror. That was just unexpected for me.
Also just remembered what I think is actually the freakiest, most unnerving part in all of TNG. In Parallels when there's all the ships at the end and suddenly we see Riker from another universe who says that the Federation is gone and the Borg have taken over. This is Riker, who is willing to kill Worf and endanger thousands of universes just to get out of his. That really sent shivers down my spine. After the episode finished I just sat there feeling really weird for ages like when you have a weird dream and you can't function all the next day. Even though it's not our universe or even 'our' Star Trek universe I couldn't get it out of my head that it did exist where the Borg won. *shivers*