For all the jumps and scares in that game, the biggest scare in the entire game for me was right near the start when you're down in the sewers I think. There's a set of double doors and as you approach them a big armoured guard kicks them open. I ended up probably emptying an entire clip into the ceiling where I'd jumped, swung the mouse up and clicked at the same time.

edit:

This was also the first game I ever actually got scared whilst playing too.