has a non horror game ever had a moment that scared you

The first time I beat the Elite Four in pokemon yellow and then saw that i had to fight Gary RIGHT after that. @_@

(i won by the way... my charizard vs his blastoise.... I spammed dig and fly)

 

the new Tomb Raider when you suddenly get caught from the trap and the dogs
Devil may cry sometimes
Skyrim
Far Cry 3 at times because of those damn guard dogs.

 

All of the Resident Evil games used to freak me out, Mine craft - them damn creepers and Amnesia, which is for the PC.

 

Any time you have a countdown in any final fantasy game, because you know you'll be stoped every five steps to fight some monsters and that there will be at least three times you wont be able to run away, meaning you MIGHT just make it with one minute to spare if you leveld up your characters enough to kill them in as few hits as possible.

 

The twisted metal games. The artwork for the early games scared the crap out of me.

 

Yeah, that Lavender Town music is pretty damn eerie, but the Pokémon games are good at creeping you out when it comes to those such moments.

The most recent being in Pokémon X and Y:

Spoiler

If you go to the second floor in a certain building in Lumiose City, as you get off of the elevator the lights start flickering on and off. This woman appears behind you and walks pass you in a way that looks like the game is glitching. She stops at the bottom of the screen and says "No, you're not the one..." and walks further into the room offscreen. If you search the room though, there's nobody there of course.

It caught me off guard. o.o

 

Aaah Pokemon can be really freaky, but I love it so much.

I also have to mention the piano in the Mario 64 Ghost House level. Scared me away for days!

Oh, and Majora's Mask. Even though I absolutely adore that game and its one of my favorites now, when I first played it, the impending doom coming from the decidedly Uncanny Valley-like moon scared several things out of me that I don't care to talk about.

 

Literally every second of the Cortana level on Halo 3. And any time I see a giant spider on Skyrim.

 

Homeworld: Cataclysm— the game is terrible, but the Beast scared me for literally 3 years of my life. I would not play any Homeworld game for that long.

 

Not a video game but...AQ. That was a long, long time ago. It must've been the only time when I got creeped out by a non-horror game, but the shock lasted long enough.
(Partway through battle the enemy will drop their skin without warning and a clone head of your character will materialise...)

 

In Dark Souls there is a giant tree boss called the bed of chaos. It killed me around 6 times and I was scared of how angry a video game had made me.

 

Oh god, this all the way.

*Me showing my friend Halo: CE*
*We get up to the part where we are introduced to the Flood*
*I pause the game*
Me: "And we're done!"
*Friend pushes escape and unpauses game, Floods everywhere*
*I pause the game again*
Him: "are you scared?"
Me: "Yep"

 

That was when Halo turned from FPS into Survival Horror. The Flood were terrifying.

 

Ocarina of Time and Majoras Mask + Redeads = no sleep

There is also that one part in Bioshock Infinite with that completely unexpected jumpscare, I literally jumped out of my chair when that part popped up

 

When I was younger I was scared of metroids. When I first saw one I started shooting everything I had (completely missing the Ice beam) but nothing was efffective. Then, when it grabbed me I didn't knew what to do and I died. After some tries I used the morph ball bombs and everything was easier.

 

Okami scared the living crap out of me. It was that level with the ghost ship, where that priest is with you. I can remember being in a room, and the floating head of the spider queen was blocking my way out. I spent at least ten minutes trying to figure out how to get past it without touching it, then just ran through it having run out of options. If the spider queen hadn't been terrifying enough, her ghost popped up and covered the ENTIRE SCREEN. I spent that whole level yelling at the game.

 

Hearing the Enderman stare noise for the first time. To say I bricked it would be a understatement.
Also this noise sends shivers up my back every time I hear it:
http://hydra-media.cursecdn.com/minecraft.gamepedia.com/0/08/Cave10.ogg

 

The river scene where you "fight" the Sorrow in Metal Gear Solid 3 is pretty freaky, especially if you get hit by the beam and that ghost face screams at you.

 

Oh, I remember another one!! When I was little, Banjo-Kazooie's Mad Monster Mansion level always scared me and I couldn't play it at all!

 

Anytime I hear a spider noise when exploring an abandoned mineshaft in Minecraft. >_>

There's been a few moments in World of Warcraft too, like when a Whale Shark decides to nom you as you're questing.

In Borderlands 2, while in the Caustic Caverns doing the first quest, stop in the Varkid nest cave to sell in that vendor in the room, having your sister tell you to just go in the room, because the larva will be fine. Then a few minutes later, coming out to Vermivorous staring at you, and you realize you guys are screwed because there's no way to kill it and you're trapped until the quest is done. >_>

The Xenosaga series has quite a few scary scenes. Can't really pick a single one though. I remember when I played the first time, when Shion sees the past, and walks into her mother's room at the hospital, oh hell no.