I'm probably stating the overly-obvious, but atmosphere definitely helps. I remember playing Silent Hill 2 years ago and found myself too scared to play alone. I never knew when a mannequin would be dropped on top of me while running about town. I'm still creeped out by it today; it's not that "OMG! Go Away!" scared, more like "Roller-Coaster-Thrill" scared. I always wanted to see more.
Survival/horror games also need a system similar to that of Resident Evil 4. Limited supplies, but always a way to manage; great combat, but still show a bit of weakness and limitation; and proper use of QTEs ::Yahtzee slaps me in the face:: ...er, maybe no QTEs.
The one thing I don't want to see out of survival/horror is what happened to Silent Hill: Shattered Memories. Okay...granted it does utilize interesting concepts and gives the feeling of weakness, but then...where's the combat? All that leaves is straight horror, no means to fight back. I mean, even in all those "Jason" movies the protagonists found a way to stop Jason, and it wasn't by endless running. James Sunderland wasn't a spectacular fighter, yet he fought back! Whether figuratively speaking or for real, he fought his way to the truth.
Okay...massive rant...but this whole thing boils down to this: great atmosphere, great application of combat, and a proper balance of running and standing-your-ground.