What's the first video game that freaked you out?

System Shock 2 and Clive Barker's Undying, I think.

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I literally jumped... twice.

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The beginning of Beyond Good and Evil with the first boss fight. It was called the DomZ Petrolomax I think I forget and forgive me for spelling it's been years since I've played the game. Anyway it scared and creeped the ever loving shit out of me. 
 
   
 
That's it in the background. Found this pic while browsing the Giantbomb news articles. It's still creepy as fuck. 

" As far as mentally disturbing me, Silent Hill 2 was just a big mind F--- for me but, I loved it and wanted to play it over and over. For jump scares, that goes to DOOM 3. People didn't like that the flashlight wasn't attached to a gun, but I think it just added to the "Oh, god! Something is behind me but can't see it while I attempt (poorly) to shoot it." atmosphere. That game was so dark. "

Diablo 1 with the Hellfire Expansion (by Sierra).
 
One of the BGMs got really creepy and I had a short panic for no real reason, doesn't help that I like to turn off all the lights at night while playing games.
 
Fatal Frame 2... Well fuck I still didn't finish the game.
 
Played the first FEAR like that too... Only played it around 11 PM till 2 AM (That's how I roll with horror games). Shit freaked me out a couple times.
 
I like to watch other people play Horror games to be honest. I like em, but I just don't do well playing them.

The dogs through the window in Resident Evil

" Tomb Raider used to shit me up. "

Aside from the fact that i was scared of Wolfenstein 3D when i was really young (like 3-4) id have to say it was FEAR. There is also one particular level in Thief: Deadly Shadows that was more or less made to mess you up, but im fair sure FEAR was around first.

James Bond Jr. on the SNES. on the very first level you can skip the ending cinematic and go onto this weird glitchy fall through time and space. i thought i was a genius haha. can't embed this video (firefox problem?) but here's the link.

metroid prime, the first chozo ghost freaked me out big time

"the game over screen on Spyro 2   "

" MYST   paranoia.... <.< >.> <.> "

Probably Banjo-Kazooie when you went save and quit and you got that cut scene where Grunty activates her machine and steals Tooty's good looks and makes her ugly. I was 10, probably too old to be freaked out by something like that, but that was the age that I was also convinced that aliens were coming to kill us all (thanks to my teacher making us study the War of the Worlds).

The god damn Alert sound in MGS always made me scared to get caught. 
 
AND THOSE DOGS in Resident Evil (can't remember which one it was, I was really young). You know, I think they jumped through the windows?

The "zombies" in Ocarina of Time. I would close my eyes and ears when they came up when others played it. D: 
 
I turned the volume all the way off when I would play it.

" The god damn Alert sound in MGS always made me scared to get caught.  AND THOSE DOGS in Resident Evil (can't remember which one it was, I was really young). You know, I think they jumped through the windows? "

Amnesia: The Dark Descent. In all other games, you fight against the monsters, and they rely on sudden scares. Amnesia is the first game where I was afraid to move forward, and that was just the demo, and after I saw a playthrough of it. Props to Frictional Games.

Return to Zork. I'd never seen video-captured actors in a game before, and it still creeps me out just thinking about it. 
 
Also, I can't remember if this came out after or before Zork, but Alone in the Dark was probably the first game to truly frighten me. 

Resident Evil 4. Those black things with the huge ass teeth..who walked hella slow...god that scared me..the breathing

When I was 8 or 9? the hallway scene in MGS with Gray Fox freaked me out.  Now that I am older barely anything creeps me out, except for Dead Space.

The original Doom because back then I knew nothing like it and was used to playing super happy fun time nintendo games.

I don't know why, but the early Final Fantasy battle cues (The quick zoom in with that screeching sound) bothered the hell out of me. Yet I don't know why. 
 
It was Final Fantasy 6 actually, I was 5 years old when I played it first, and it caught me off guard. I was 5 years old and stupid! Give me a break!

The first time coming to future Castle Town in Ocarina of Time really got to me. It was a perfect storm, going from bright colors, cheery music, and lots of people and activity, to browns backed with eerie music, and slow shuffling zombies.

Resident Evil 2! What a freaky game.

The earliest one I remember was Jaws on the NES. I'm still ridiculously afraid of sharks in video games.

The Game Over witch scene in Banjo Kazooie.  first time i had seen something like that.

resident evil 2, it was pretty creepy i thought. the windows breaking i wasn't expecting that and it scared me. 
 
another game was fear 1. the girl would just come out of no where.

I played Ocarina of Time when I was pretty young. The Wallmasters in the Forest Temple really terrified me for some reason. I was almost too worried to finish the game. 

Do you know what freaked out me?  The original Metal Gear Solid's sickly dark-blue and green colour palette and it's fluctuating, pixilated PlayStation graphics.  It was really unnerving when I was younger.
 
But now, for some indeterminate reason, I'm not usually scared by games.  Although it has been awhile since I've played a proper horror game.

" The atmosphere of the original Diablo really unnerved me as a kid. That was, what, '97? I was nine. That shit was fucking overwhelming.  
 
Ah. Fresh meat. "

First arcade game that freaked me out was Altered Beast. 
First console game was Drakkhen on SNES.

" @Sir_Ragnarok said:

" The atmosphere of the original Diablo really unnerved me as a kid. That was, what, '97? I was nine. That shit was fucking overwhelming.  
 
Ah. Fresh meat. "

This. I used to always watch my older brother play it and when I tried I'd freak the fuck out when I got to The Butcher. "

Metroid Prime 2, those aquatic lizard things that ran around on two legs in the Torvus Bog really freaked me out because they always attacked me from behind.

I was 12 when RE4 came out, probably 13 or 14 by the time it came out on PS2, which was when I first got to play it. The Regenerators in that game scared me during my first encounter with them. All you hear is the sound of a gurney being knocked over, and then that heavy breathing, until finally the thing looms out into view, and you realize that even if you shoot its legs off they'll just grow back.

Majora's mask, Playing majora's mask after oot as a innocent little boy was just creepy and depressing as hell.

Metal Gear Solid during the Psycho Mantis fight. How do you know I likes me some Castlevania ?   I really freaked out when I thought my TV was spazing out because it kept switching over to Hideo mode during the fight. 

I guess Silent Hill 2 and Condemned are the two games that have freaked me out the most, both in different ways. But, the first game would probably be Doom or maybe The Legend of Zelda: Ocarina of Time. The ceiling-monsters in the forest temple always makes me nervous to this date and when I was a child, those things were fucking with my psyche, big time. The awesome, but really creepy, background music did not make it any easier to overcome.