Well, are we talking best game overall in the survival horror genre, or scariest game in the survival horror genre?
For scariest, I'd say either Silent Hill 2 or Eternal Darkness. Both are very good at what they do, which is to be scary/unnerving.
For best, and these games really stretch the "survival horror" genre, I'd say Resident Evil 4 and Dead Space 2 (both series were on the poll). I adore these games. Not because they're scary (RE4 really could have been, and it had moments), but because they control so goddamn well. They're controls keep me coming back to them again and again. I can't even count the amount of hours I've put into both games. I wouldn't classify either one as survival horror, but the general public would, so you know what, I'm counting them!
Oh, and I loved Doom 3. It wasn't scary, but it was a fun game.