What makes a good, scary, atmospheric Horror game?

Ambient noise and scary music!
and don't forget games like Resident Evil (1, 2 and 3)

The feeling that there is always something around the next corner.. and just when you feel you're safe and in a well lit place, a shadow monster appears. Just a shadow on the floor and walls with a whisper. Also urgency, like the water monster in amnesia.

I havn't played amnesia, just watched an enormous amount of let's plays and really like the idea. I would add something hostile ( enemies) as a only jumpscare game, well it's just not my taste ^^ Being a fan of dead space and a bit of the Fear series I would recommend, if you add weapons make them either rare with for example durability meter, having not much ammo (talking about guns which would add something of survival to the gameplay) or weapons who are not lethal, only to hold off an enemie and give you time to escape or hide. To powerfull weapons (or to much ammo) tends to withdraw the horror atmosphere for myself and you have not a feeling of vulnerability as in Amnesia for example. As for humans and/or sanity meter: that depends on the story. You could perhaps transition from human enemies into something supernatural or leave them human beings. A little point I would like to see in a horror game is actual (and multiple) choice making, perhaps under pressured conditions wich affect the entire fallowing story telling and ending.

If more comes me to mind I'll add in my post ^^

Honestly I feel like F.E.A.R 1 was ALMOST there, add in some aspects like a sanity meter and you would have a winner.

Do not add Weapons if you want to make it a survival horror.Add enemies, Sanity meter, Ambient noises, dark atmosphere. The only thing that scares me the most in horror games is the dark atmosphere and the ambient noises.

Lack of weapons. The scariest game I've ever played was Haunting Ground on PS2, because you can't fight, only run and hide.

Maybe you also want to check out Silent Hill series. It's also scary, but in a different way. IMO its whole atmosphere is scary rather than having things popping up suddenly.

Call of Cthulhu: Dark Corners of Earth had quite the horror feeling when You had to deal with the character's sanity dropping when he sees disturbing imagery and is under a lot of pressure, also, make sure that there is no ammo counter when You're holding a gun (only an option to take out a mag, or look in the chamber to see if there is any ammo, like Condemned: Criminal Origins had), and of course the style that Mafia used, that when You reload Your gun, if the mag has any bullets in it, then they will be lost. That gave the game a good realism as to the situations when You were going right around the corner and You had to decide if the bullets in the mag will be enough for a quick takedown.

All that, and a lot of other ideas and You will make a quite decent game. Of course, good luck! ^_^

the element of surprise obviously

What about tentacles?
Now, I've enjoyed reading a lot of Lovecraft, and I can say that a few important points to instill fear on the reader/player/watcher, is the feel of uselesness and confusion or unknowing, and maybe knowing that you have no hope, but keep trying anyway.
Enemies? Yep.
Precious sanity to be lost? Oh yeah.
Human? If you refer to NPCs... maybe, but knowing that you are alone is kinda scary.
Ambient noise? Yes.
Weapons? It really depends, but that's a no from me.
Aaand that's pretty much all I can say, good luck with your game!

The feeling of being defendseless against an unknown thread