Most unnerving scenes
Much as I like the Francis Bacon-inspired spinning heads and the hospital scenes with deformed and mutilated bodies, to me that most effective and unnerving scenes are the more subtle ones. I'm referring to those scenes where Jacob is dealing with someone who seems (mostly) human, but there's just enough "off" about them to suggest that there's something demonic under the surface. In other cases, less would have been more, particularly early in the film.
For example:
1. The old woman on the subway who just stares into space when Jacob asks about the last stop. The homeless person with his face covered on the subway seat was good too, I think that for such an early scene, just showing his thrashing and the covered face would have been unsettling enough without the reveal of his "tail."
2. The full subway car that Jacob has to dodge. But once again, I thought that showing the mouthless face at the back of the car (figure waving at Jacob) was a little excessive for such an early scene, just the strangeness of a full car of passengers staring as they pass him by at a very late hour would have been sufficient.
3. The scene in bed with Jezebel where she runs her nails down his back and asks "What were they, Jake?" when Jacob says that the people he's been seeing aren't human. Something seemed off about the tone of her response, just enough to put you on edge.
4. Jezebel's tantrum ("IS ANYBODY HOME" - mentioned on another thread). For just a moment, her eyes are shown as jet black, with no whites.
etc.