Games tend to have moments that really make you uneasy or consider taking a break from it for a bit. It can be anything from cutscenes or enemies to even just areas or music that gives off a disturbing feeling but no matter what its still rather creepy. I'm kinda aiming for these to be less from horror games and more so in games where it felt out of place as it adds to the creepy factor (and using a horror game is kinda easy for things like this) but if you really want to use one I won't yell at you :p. I myself can't really think of one to share right now but I would love to hear from anyone else. 

I can remember some creepy video game moments from when I was younger. In Grand Theft Auto San Andreas, I was walking through the desert looking for things to do when I found a bunch of body bags in a hole. That just sent shivers down my spine for some reason and I thought that was weird. There was also a ghost in Hit man: Contract that I had heard about and tried to look for it. When I found it, it really surprised me and found it really odd.

The hidden message in Sonic CD. A friend told me of this one, he said that I needed to calibrate the sound in a certain way. He told me how to, and then, after pressing 'A', this REALLY unnerving screen comes up with creepy music, an evil laugh, multiple Sonics wearing clown masks, and a Japanese text that say "FUN IS INFINITE, WITH SEGA ENTERPRISES - MAJIN"

What the heck, Sega...

There are vids of it on YouTube, if you feel like checking it out, it's quite imfamous!

Caves with no light or random enemies popping out of nowhere. Main reason for caves is because you always have to wonder what is ahead of you or behind you so it is always trying to keep you alert then in some games it is like nope nothing to worry about in this dark cave. With random enemies popping out of nowhere is self explanatory. Like this one time I was playing skyrim and I heard a door open behind me and when I turned around a draugr was right there and it made me jump some.

That one boss in Super Mario Sunshine, Eely Mouth's Dentist. It scared me so much as a kid, that I actually had to have my sister beat it for me. Just look at him! He's too creepy! And the boss music fits the theme too, look it up on YouTube, for the boss music.

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The SA-X in Metroid Fusion for Gameboy Advance. That thing is so intimidating. Not just the disturbing close-up on its face, but just exploring the game world and then suddenly entering a dark room and hearing nothing but those ominous footsteps...it scared me as a kid, and it still terrifies me to this day.

Ah, creepy elements in video games, where do I start? Well, in Super Mario Galaxy 2, in the lava galaxy, you can zoom in on the background, and notice three strange figures watching you. People believe they're ghosts. Later in the stage, check again, they're still there.

On Mondays, I believe in Animal Crossing: New Leaf, at five in the morning, an odd television program is on. Turn on your TV to find an alien trying to say some sort of message.

Also in Animal Crossing: New Leaf, there's a town known as Aika Village. I'll just give you the abridged story. This town has creepy villagers such as Shari, but also a mysterious girl named Aika. She'll only say, " I love my mommy" in Japanese text. On the beach, there's a random pair of shoes. It's common in Japanese culture for someone to take off their shoes before committing suicide. The houses are just flat-out creepy, but this video will speak for itself.

http://www.youtube.com/watch?v=0mecyfRa15M

The strange ghost at the end of the Ghost House level in World 4 of Super Mario 3D Land. To be honest, things seem creepier to me when they are in "Family-Friendly Games," such as Mario, Sonic, Kirby, etc. Below is a picture of the ghost in the game.   Note: To make this appear you must wait about 30 seconds at the VERY END of the level, and it will appear. If you can't see it, it's above Mario in this picture.

Check out this ghost sprite from Final Fantasy VI.


I actually thought the sprite was pretty awesome, but my sis-in-law told me she found it incredibly creepy and wished I hadn't showed it to her.

Other than that, the ending to The Company of Myself is a real creepfest, especially combined with some telling scenes from its prequel, Fixation. I can't really explain more without giving away plot points, though. Let's just say that Fixation is subtle, and the more you think about it the creepier it gets.

Mimi from Super Paper Mario scared the crud out f me when I first saw her true form. Or rather, the transition into her true form.

The first chapter in Clock Tower 2 scared the crud out of me!  There are weird yellowish severed body parts hidden everywhere!  Plus the little girl won't die!!!  It's just super creepy!

That one shrine in Ocarina of Time where the Sun's Song is found always, ALWAYS scared the bejeebers out of me.

The Great Fairy in the N64 Legend of Zelda games.  She is incredibly creepy, and needs to put some clothes on.  Her, and Tingle...Tingle is creepy, too.

But maybe the creepiest character in the LoZ series is the shopkeeper from Skyward Sword.  He is very...er, different.  I just wanna run as far away as I can from him....but I need dat shield...

supernerd117 :   I agree with you 100% The great fairy .. I always thought she looked kind of naked and her laugh was kind of creepy to me as well. Tingle I always thought he was a rapist or something. I have no idea what Nintendo was thinking haha Last but not least that shopkeeper he always has that weird grin on his face and follows you around. I use to say to myself " Why does he have to be the one you have to buy the shield from ? " In general Zelda always had some creepy stuff in it.

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When I was kid I use to play F-Zero X on the nintendo 64. I use to love playing that game on expert and had a favorite racer. It was a guy but every time I would fall of he course he would scream like a woman. After playing the game for a long time I realized that most or some of the guy characters that would fall of the stage sound like the same woman. I don't know if I had a messed up copy of the game but I found that to be funny and creepy at the same time.  

I always found the undead naked zombies in Ocarina of Time to be extremely creepy. When you get attacked by them they jump on your back and scratch your face which also looks like they're humping you from behind. Seeing that when I was younger gave me a nightmare once and I didn't play that game for a whole 2 weeks. I remember it like it was yesterday.

Odd flames : when i frigen saw lavender town the moment i stepped in that place a cold chill ran down my spine

One game that scared the hell out of me was Metroid Fusion. It had a truly creepy atmosphere (what with Samus being stalked by some creepy clone) and some terrifying elements.

The 2 things that scared me the most were the SA-X and Nightmare.

First, the SA-X. 

Then there's Nightmare.

Yeah. Scary. Pic 2.

Even scarier. Pic 3

I found Dr. N Tropy from Crash Bandicoot 3 creepy as a kid, and even today. The way he walks out of the pitch black background and the noise hos gears make un nerves me today for some reason. Also, his appearence, with his blue skin and sharp eyes, scared me a little.

Just... the general atmosphere of Sonic R. I loved that game to death as a kid, in fact it was my first game, but sometimes the music would stop and it was just unsettling to me.

Probably the most memorable "creepy" game I have ever played, has to be the first Resident Evil. The entire game oozed creepiness. Even right from the start, it was creepy. With the voice saying "Resident Evil" in the creepiest way possible when you clicked "start". The first "jump out of your skin" moment was when you entered the first side hallway I will NEVER forget!!! The dogs!!! You're just walking along the hallway. Thinking nothing will happen until your reach the next room.... then BOOM!!! Dogs burst through all the windows and proceed in trying to kill you!!!

Opening doors into a room you never been in... hearing the creak of the door as the room loaded up. Walking up onto zombies hunched over a dead body eating it... and it turns its head and sees you as his 2nd helping. Every boss monster in the game getting bigger and creepier as you go through the game. All the times it was "too quiet"... just to surprise you at every turn.

Yes.... I would have to say, In my opinion... Resident Evil is my number one pick as creepiest game ever. Kept me on the edge of my seat the entire time playing it.

In Super Mario 3D World, Mario (or the other characters) can collect a power-up called the Double Cherry, which will split Mario into two.

If the real Mario dies, the Mario clone becomes the real Mario. Let that sink in.