I found any place that had spores absolutely creepy and i couldn't wait to get out of all the areas with spores. The hotel basement was beyond the scariest part. I watched a gameplay vid on youtube and the girl playing was actually crying trying to get past that part. Oh and the areas where you can hear the bells tolling, there was one i believe in the Winter section when Ellie was trying to escape Davids people, and one earlier on in the game, they weren't particularly scary but just really eerie. The David fight with Ellie was scary when he came at you from nowhere. The whole winter section was quite scary for me, when the blizzard came and you could barely see. Trying to sneak past clickers is always scary for me. And the last part with Joel running out the hospital i was frantic on my first try looking for the way out. I'm pretty much a wimp.
I loved the flamethrower though, i guess it's up to the player how much they used it but i went crazy with it
The first encounter with the Clickers in the subway had me sweating and holding my breath but once you know how to deal with them the Clickers arn't so scary any more.
The Stalkers on the other hand are more unpredictable and are always scary for me. They are part of the reason that the Hotel basement is scary. From the masterful build up of tension (rats running towards you, spooky noises ect) to the perfectly timed jump scares the whole Hotel Basement section stands out for me as a fine example of survival horror.
Also, the David fight isn't that scary (for me at least) if you use listen mode to see where he is.