I can't think of many games that scared me the most. Resident Evil comes to mind, it was definitely a game I found scary back in the day. But, that's not the first game that comes to my mind. Dino Crisis 2 for Playstation 1 on the other hand was a game that made me jump and kept me on edge thoughout my journey surrounded by the run down buildings, buildings in general and various other areas filled with vegetation and abandonment, rusted fences/gates, bloody stained floors/walls etc, worn out machinery, corpses (Also covered in vegetation and what not) etc. Pretty much what the world would look like if all the humans on our planet were eaten by dinosaurs (Now, that's a movie waiting to be made).
I can't remember the names of the characters but within the game you have good variety of weapons to choose from or find along the way, obviously you have dangerious mission obectives which vary from finding key cards to taking down a T-Rex to get to the next section, mysterious plot twists to keep you interested and curious throughout the story (Such as scientists experimenting on dinosaurs) and best of all the many types of dinosaurs that want your blood.
Of course, the biggest dinosaurs in the game were pretty much lead to big boss fights every now and then and boy, they were scary back then, at least for me they were. Dino Crysis's plot is very similar to Resident Evil, just with dinosaurs and not zombies. There's also a cinimatic element to it also, quite similar to Resident Evil 1, when you're inside the mansion. Dinosaurs even get experimented on in the series, in Dino Crisis 3 they get turned into half dinosaur and half machine but that's a whole other story (A story I can't get into because I'm really struggling to remember the Dino Crisis 2 story let alone the games released after it). And, what you do with the main character in Dino Crisis is similar to what you do when playing as Leon S Kennedy in the old Resident Evil games.
I've never enjoyed playing a horror game more than I did Dino Crisis, it will always in my heart! No doubt the other reason is because the main character 'Regina' is super sexy! Dat 90's vibe though! She looks a bit like Major Kusanagi from Ghost in the Shell.