These are the ones which get my vote (despite the fact that I can watch them unflinchingly, and not hide behind the sofa)
TNG: Conspiracy, Where Silence Has Lease, Night Terrors, Identity Crisis, Violations (even though Beverly screaming like a little girl was unintentionally hilarious), Schisms
DS9: Empok Nor
VOY: Faces, this is one necessarily scary per se but more f*cked up the way that the Vidiian scientist kills that goldshirt and grafts his face on. It's just not something we expect from a prime-time TV show. Plus, it really gives us the impression of how 'alien' the Vidiians are in their way of thinking. The Thaw, One.
ENT: Fight or Flight. I can't blame Hoshi for screaming like a 12 year old when she saw those aliens hung up on meathooks with their bodily juices drained out!