Now, first of all this is a personal list and thus you may disagree that some of these even count as "scary". Second of all, as I mentioned I'm not a huge fan of horror so most of these are from non-horror games - as such, they are probably scarier for me within the context of the game. Now, without further adieu, let the horror commence!
There will be spoilers...
5) Spider-Man - Monster-Ock
Picture this, you've just defeated Doc Ock and Carnage back-to-back. Spider-Man poses heroically as he begins his "it's all over" monologue when suddenly...
The result of Carnage's symbiote attaching itself to Doc Ock, turning him into Monster Ock. However, instead of fighting you have to run away from him as Ock's lab starts exploding. What follows is a very tense run (and swing) for your life, as Monster Ock chases you screaming such lovely things as "DIEEEEEEE". A part of the scariness of this boss is being constantly chased and knowing that if Ock catches up - you're dead. Although this section did go on slightly too long, it was for the most part a thrilling way to end one of Spider-Man's greatest video game adventures.
4) Heavy Rain - The Lizard
Heavy Rain revolved around the story of Ethan Mars and how far he would go to save his son. Many of his tasks involve a little sacrifice or risk of death. The Lizard, however, is the one everyone who plays it will remember. You're asked by the origami killer to cut off the top section of one of your fingers, on camera, in order to get the next clue to your son's location. You're given a wide variety of tools to help you do it...
It's one of the hardest to watch scenes in gaming history. It's made worse by the fact that you have to do it yourself (or at least, move the analogue stick to perform the action). It's not "horror" in the traditional sense but there are very few scenes in video games that are more unsettling.
3) Resident Evil 2 - Start of the Game
I'll be honest, I've not played a lot of RE2. Despite this, I still remember the very start of the game and how tense that was. After the opening cinematic, you're left to fend for yourself. The game isn't saved, you have no healing items and very little ammo. You have to run from most of the zombies, but they are relentless.
Through narrow alleyways, buildings and even an abandoned bus you will have to decide whether to fight or flee the hoarde of zombies. Try to fight them all you'll run out of ammo. Run away from them all and you might miss some useful items. Nowhere is safe until you reach the police station and with it, the first save point of the game. Horror games love to remind you how powerless you are at the beginning of the game, but RE 2 did it better than any other.
2) Metal Gear Solid 2 - Arsenal Gear
This one is definitely a personal moment. I was eleven years old when I first played Metal Gear Solid 2 and I was loving it. It was my first entryway into the Metal Gear series and it was quickly becoming one of my all time favourites. Then I got to Arsenal Gear. Running around as a naked Raiden was funny at first but then I started getting codec (MGS' version of the radio) calls like this:
Being a rather idiotic eleven year old who did not quite understand the whole "fourth-wall" thing, I did. Embarrassingly, I then had nightmares about this - though the specifics of them I do not remember. Young me simply was not ready for crazy Colonel Campbell and when I did find the courage to play on it didn't get any easier until, as always, Solid Snake showed up to save the day. Even today, I am a little unsettled at this whole section as an aftermath of the effect this had on eleven-year-old me. But ten years on I am a braver man now and I'm not gonna let some silly video game scare me int...
AHHHH.
1) Alan Wake
This one is a bit odd because it's not a particular moment that was the scariest. You see, the main gimmick of Alan Wake was that the darkness is unsafe. Enemies are essentially shadows until you shine your torch on them and make then vulnerable to death. The only times you are safe is when you're in light. So, the reason this is number one is due to the psychological effect this game had on me every time I stopped playing. I tend to play games at the dead of night, just before going to bed. I played Alan Wake every night for a week. I would then go to bed. In the dark. After spending a couple of hours training my brain to fear the dark, it would take me a while to switch back to reality.
Alan Wake is a really good game, but isn't that scary. The game itself calls itself a "Psychological Action Thriller" which is a fair description. However it does a brilliant job in conditioning your brain into fearing the dark and that is why it's my number one "horror" gaming moments - because the rest of the list may have been scary within the context of the game, Alan Wake was the only one (bar MGS 2, which can be explained by me being a child when I played it) that truly affected me out of the game. Kudos, Remedy.