Some on my list may not be that revolutionary, they just creeped me out.
Silent Hill series: Self explanatory. The series never fails to choose the places that look creepiest at night: schools, hospitals, amusement parks, prisons, etc. I've found SH2 the best, but the scariest is either SH1 or SH3. I won't go further because everyone knows this series.
Amnesia: Again, it's popular so I don't need to explain much. The game is what I call "hide-and-seek" horror, which can be scary at first, but then ends up being ok when the player decides to "Leeroy Jenkins" the level. Amnesia somewhat accounts for this by introducing the monsters later in the game and adds the effect where staring at the monsters reduces your sanity. The messed up sounds playing when sanity falls also spooked me.
Fatal Frame: MY WINNER FOR SCARIEST SERIES. Pokemon Snap Benadryl Edition. The gimmick of this survival horror is a camera used to defeat enemies. You do more damage by keeping the camera on the ghost or timing your shots in the midst of an attack. Ghosts can appear anywhere, shifting through walls and keeping you more on edge than other survival horrors.
Like Silent Hill, the series makes use of a terrifying atmosphere, but they do something different that I can't explain. I know it's just a spooky haunted house but I'll give an example: imagine peering out the courtyard of a mansion and getting a glimpse of a malevolent looking onryo staring right back at you waaaaayyyy on the other side of the courtyard. Now you know that thing is wandering the same building in which you are located, and it's only a matter of time for when you encounter it. There's plenty of scares like that which just brings dread. That coupled with the disturbing ambient sounds makes this game a struggle to complete alone at night.