I'm not too sure. The only thing that kinda scares me now are zombies. I wasn't always scared of them, I even used to joke around with my friend when he admitted zombies scare him just a few years ago. Then he more or less explained to me its because of how you would literally have to face people you know and care about for your own survival, now I can't shake that thought.
I think out of your example the first might apply best. Dark unknowns. It really helps if you set up some sort of recurring powerful enemy that it is certainly better to run from then fight. Something like the Tyrant from Resident Evil games, even when it's obvious the Tyrant is gonna jump you it sucks when you know you have to go past it to proceed. If it jumps out from an unexpected area that's even better, as long as that's not overused.
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