Trying to think of ways to revive this thread...
There's a lot of stuff which hasn't been discussed, I'm sure. We've been over the bulk of the typically considered "scary" episodes in TNG, but what about individual moments? Again, what about episodes such as "Remember Me" which is never remembered as scary, and yet it is absolutely terrifying in some ways?
We don't have to focus solely on TNG. Although it's in the TNG section, I don't think it matters if stuff is brought up from other series, does it? So long as it's about Star Trek. For the most part, though, I do think focusing on TNG is a good bet.
How about episodes which are more existentially creepy or frightening, as opposed to directly so? Under this, I would include "Skin Of Evil", "The Royale", and "Allegiance", amongst others.
I still find it a very fascinating subject, the subject of horror and atmospheric creepiness in television generally, and especially in sci-fi television. It's there that some of the weirdest things can be imagined and envisaged, but most be done so in a subtle way. Although I don't remember having yet seen any of it, I've heard that "The Twilight Zone" was like this at times.
Less may not always be more, but there's something about horror in space that's often so awfully creepy. Perhaps it's because of the enclosed spaces? The potential for meeting or being visited by the most strange and bizarre and terrifyingly incomprehensible aliens? Or many other things? Either way, space can be scary.