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Most videogames give the player a third-person perspective, but a second-person story. "You" is directed at both the player and character. Considering the Heroic Mime status and The Stoic character type, keep examples to sounds that occur while an enemy is offscreen, alerting you to their presence. Or another character mentions their fear. You'll forget you're safe behind your screen when you hear these...
Afraid Of Monsters has the hissing, gurgling noise that means a Twitcher is near. You can hear it through doors and around walls in many, many sections of the game. And they never come alone...
Amnesia: The Dark Descent: The terror music, which signifies that a monster is chasing you. Apart from being very bad news whenever it happens, the sound itself is terrifying, sounding like someone screaming bloody murder.
In the opening of Battlefield: Bad Company 2 when you're in WWII, half way through the mission, you hear this odd sound. The sound repeats a few times. Once you find the scientist you came to save, you hear it again. This time, the scientist FLIPS OUT at the sound. He begins saying how you're all doomed etc. At the end of the level, the secret weapon that was making that sound completely DESTROYS you, the boat you're on, and sends a huge tidal wave crashing down on you and your squad. Cue time skip to present day. Towards the end of the game, you start hearing it again. Your squad is commenting on it, and this time you know exactly what it is, and as far as you're aware, there's nothing you can do about it but watch your squad die again. Yes, the weapon goes off and practically LEVELS the city, but your team is Made of Iron, so they survive.
In Dead Space 2, a particularly memorable enemy will give you a temporary phobia of chirping and whistling, as it signals the arrival of a pack of a particularly lethal and hard to kill strain of necromorph.
Descent has the shrieks and cries of the robots. Most aren't too bad, but the Class 1 Drillers make an extremely shrill noise like a badly damaged car starter, and given their status as Demonic Spiders, it just enhances the dread you feel when you hear it. There's also the "ZRRN!" noise that Mook Makers make when they activate; hearing that sounds almost always means you're going to quickly have a nasty fight on your hands.
Don't Starve is chock-full of "the hell was that?" sounds, especially when you start to go insane. A creepy music box chime symbols that the darkness is about to get rather unfriendly. Even the player character gets unnerved and remarks at the sound of Hounds or the Deerclops coming near. ("That sounded big!")
The Shrieks of Dragon Age: Origins are fast, vicious, travel in packs, can stun and "overwhelm" (pin to the ground and maul until dead) your PC—and you can tell they're in the area by their ear-splitting screams.
Skyrim: the flapping of wings informs you of any imminent dragon attacks. Brought up in the prologue, where soldiers comment on wondering what that noise was.
The weird echo/thunder like sound you hear when a dragon is nearby.
The creepy shuffling noise of a frostbite spider walking around, especially when you can't see it, is horrific, especially if you already have a fear of spiders.
Enemy Zero is a game full of Demonic Spiders: Invisible aliens that will kill you in one hit, and your only weapon requires charging to use (but not too much charging or it shorts out and you have to wait to use it again) and can only be used at point blank range. Your only method of staying alive is a radar that tells you when an alien is nearby with audio pings. Thus, hearing that "Ping ping ping ping ping" get faster and faster is the scariest damn thing in the game.
Fatal Frame Whenever a ghost is about to attack the normal music changes to really scary music accompanied by the noises of said ghosts. The scariest is Blind maiden who's music is accompanied by horrific screaming
There's something that sounds like a wheezing, whispery voice, or a heart stopping screechy sound whenever Alma is nearby. Then there's Alma's music box, (listen to it here). That horrible, sad, upbeat, painful, tear-inducing, pants-browningly chilling tune. It's like someone scientifically formulated the perfect theme song to emphasize every single aspect of Alma, and then used it in the most disturbing manner imaginable.
Child Alma's trademark deranged little giggle.
In the locker rooms of Wade Elementary you are attacked by ghosts that are hard to see and they make this horrific noise. Plus the horrible rapid-fire slamming sounds of the double doors, making it hard to hear anything coming at you, and they steadily grow louder and louder as you get closer. The noise itself is just plain disturbing....
The game also pulls off a few audio stings when certain scary elements come into the field of vision. It's also used - in slightly less dramatic fashion - to alert the player to a crisp packet on the floor, letting them know that Norton Mapes is still alive.
The Scare Chord played when the automated gun turrets pop out of the ceiling.
Rattling objects. In the first game they can be ignored safely, because it's possibly a malfunction of the collisions engine, and it's only things like soda cans, chemical flasks and other small gadgets. Doesn't detract any from the scary factor, especially if you remember the common aspect of ghost stories that they lightly disturb objects whith their presence alone. And then you go through the Vivendi sequels... Where the rattlers are much larger objects, and it often means a pack of the mostly invisible Shades is out to get you. Don't be surprised if you shoot a steel drum you're walking on top of just because it scraped on the floor, especially after the nuclear explosion in Perseus Mandate. It doesn't help that you have to go through an area of the Perseus Project's cloning facility where all the automatic doors produce a sound similar to the cackle/laugh that was the only hint those near invisible shades gave you before attacking.
In the old "Frogger II: Threedeep!", the "running out of time" noise is not only annoying but loud, louder than the rest of the game's sounds. When it starts, if you're not watching the clock, it catches you completely by surprise. It only gets scarier the more you activate it during a gaming session (likely while trying for that last life raft on the surface of Level 5). And it always ends as suddenly as it starts, as the clock is literally at zero for a few seconds and then Frogger suddenly dies.
Developer interviews have noted that, upon hearing the poison headcrab hiss, playtesters would often completely ignore anything and everything else in order to find the poison headcrab, even going so far as to throw all their grenades and empty entire weapons' worth of ammo.
Every single type of Infected in Left 4 Dead 1/2 has their own distinct sound to warn you of their arrival, including a few who will switch from low growls to all-out screams or roars as soon as it has one of the Survivors in its line of sight. Each of them even has their own accompanying theme music/musical cues whenever one of them is coming or doing something bad to you or one of your teammates, and because the Survivors can be overrun very quickly on just about any difficulty if they aren't attentive, listening for them is so essential that you almost can't play it without the sound up to a reasonably high level, which doesn't help a whole lot with the Jump Scares.
Mass Effect 3: The mechanical, ear-splitting, spine-chilling BWOOOOOOORRRRRNNNGH that the Reapers make. It's mentioned in the game, and supplementary materials reveal the Reaper horns are specifically tuned to produce a panic response in many organics, and indeed there's a good reason for this. Low-pitched, loud sounds (like the growls and roars of many animals) and jarring, irregular sounds (like a scream), incite a fight-or-flight reaction. The sound of the Reapers combines these two qualities just to make you shit yourself. The audio team deserves a goddamn medal. In fact, they did research on the kinds of noises that most scare humans and then combined them for the Reaper horn. So it is a compilation of the scariest sounds known to man.
The Banshee scream whenever one enters the battlefield. Also to some players, the sound of their teleports can be even scarier, as the nigh-unkillable Banshees steadily advance towards you.
There's also one in Metroid: Fusion, the footsteps of the SA-X whenever you encounter it.
The cave noises in Minecraft. They're all absolutely terrifying. Now that resource packs can add new sounds, Ozo Craft gives even more ambient cave noises to shit your pants to.
Neverwinter Nights 2: Mask of the Betrayer: In one area, an insane hag is making loud screeching noises and rambling on about killing and eating people. Other characters in your party occasionally comment that they would like to either kill the noisemaker or cast Silence on her.
Secret of Mana has the hollow, freaky ghost-whale sounds of the approaching Mana Fortress. Spine-chilling when you first hear them at the start, when you don't know what they are...even more so when they show up again near the game's climax, and you now realize what they are!
Each biome just seems to have it's own mix of various sounds, from ringing cellphones and crying babies in one, to guttural foghorn calls, ghostly moans and satanic whispering amongst the sound of happy chirping birds.
Star Trek Online: In one of the missions of the "Specters" arc, you and your crew must go into the bowels of the rundown Drozana Station. Partway through, strange things happen, ultimately leading to a mysterious voice singing a song
Bonnie-kin, Bonnie-kin, all dressed in red Bonnie-kin, Bonnie-kin, soon you will be dead.
What makes this even scarier is that this was the game's first vocal recording.
"Team Fortress 2" The growl that the tanks make in Mann vs. Machine mode definitely counts. It is a deep, guttural noise that, the moment you hear it, you just know that this is going to be one of those levels.
Also in MVM, Sentry Busters. Especially hellish if you're the Engineer.
The Night phase music of Town Of Salem starts slow and creepy, but as time runs out it gets more intense as you wait to see if you live or die.
World of Warcraft, the sound a Fel Reaver makes is like some demented, hellish fog horn, followed by the screen shaking, and a gigantic mountain sized monstrosity that's usually 10 levels higher than you and an elite on top of it all charging you down.
The ambient sounds of Naxxramas are pretty horrific as well. Notable are the echoing cries of Thaddius's..."components"...
Xenoblade's "You Will Know Our Names" might be an absurdly cool song, but if you hear it and don't see the enemy you've engaged when it starts playing, you'll very quickly learn to fear it, as it means you've just been ambushed by a boss-level monster, and some of them can be upwards of 70 levels higher than you at the point in the game when you encounter them.
Nearly every noise in System Shock 2 that foreshadows an enemy's presence, but the weird humming of the eggs of the Many take the cake, since they're hidden EVERYWHERE once you get the elevator working, and that humming is usually the only warning you get before they hatch some monstrosity to chip away at your precious health meter.