The Stalker scare is more of an oppressive feeling that slowly creeps in. You don't really notice it until you suddenly hear a Snork growl or the bloodsucker sound. The ambient noise in the Stalker games is very effective at creating this initially hard to notice creepy feeling. Like something is incredibly wrong, but you can't put your finger on it. Lighting and inherently creepy environments (not to mention the creepy story) also do their thing. And the monster idle sounds. I've encountered a Burer who imitated a crying baby while he was invisible to deceive the player. That is creepy stuff.
Stalker also has monsters that are pretty scary by default - controllers, bloodsuckers, poltergeists, burers. These are scary because they take control away from the player - controllers do the view zoom thing, poltergeists do telekinesis which the player cannot counter, you can only run for cover. Bloodsuckers have invisibility and in the later games can attack you from behind, immobilize you and suck your brains out while your controls are taken away. You literally have to watch your back because they will try and circle around you. Burers can use telekinesis/psi attack to make you drop your weapon. All of these are traditionally considered "bad ideas", and players of classic FPS will whine about the game taking their control away. It works pretty well, though, because it makes you want to avoid it if at all possible. Consequently, you hide, you turn around periodically to watch your back, You're never quite safe because this stuff *could* happen.
The telekinesis is scary purely because it is extremely dangerous - it can outright kill you and you can't do much except hide, flee, or stand absolutely still and hope they go away (like a rabbit in the headlights, literally). It makes the player feel insignificant, which is why it's scary (some would say annoying). It's an ability that in other games, the player has (HL2, Bioshock). Here they give it to the monsters, which absolutely turns the table. Same for invisibility - it's like giving a ring of shadows to the monsters, not the player.
In Quake, the monsters had the chainsaws, not you. The exact opposite of Doom. Giving a chainsaw to the player evens the odds and removes the creepiness, actually.
The dogs that can summon illusions of themselves are also scary - which one is the real dog? You don't know where the enemy actually is. Very stressful situation. They can just keep summoning, and you might waste your ammo on the illusions as well. This just creates stress.
Lots of monsters in Stalker can circle strafe the player very effectively. Again this creates stress - it is part of the entire oppressive feeling. You try to line up a shot on one of them, while two others are moving in to chew on you.You feel helpless, you feel outgunned, the enemy is inhuman and relentless, you have no time to aim properly, there is a lot of pressure, you spam the medkit button like crazy, and finally you want to flee.
Stalker combines the creepy oppressive mood, the jump scares, and the truly dangerous enemies & the player's physical loss of control and consequently the wish to avoid that. In Doom 3, nothing is really dangerous. As a rule, the player outguns the monsters, like in Hollywood movies, despite all the screaming. The player has the BFG, the player has the Soul Cube, the player is a gun toting Texan. Not so in Stalker. Stalker establishes a continual, real threat, and it is not American heroism, it is the all-too-real Soviet aftermath where most NPCs are aimless and powerless and have to live off scraps and dream of the Wish-Granter.
Doom 3 and Quake 4 are like someone saying "boo!" only to add "I'm here, just shoot me. I only take 1 shot to the head." And the monsters will just stand there for way too long before actually attacking, to make sure you can get a headshot in. It's like they are only kidding. Stalker is like someone really means it, no jokes and no excuses and they DO want to kill you and they're not waiting for you to headshot them. "I'm biting your head off while you are helpless. Yeah, it's unfair. You shouldn't have come here." And you fear that situation all the time because it really might happen sooner than you think. It's sublime, but it's there.
As for having this stuff in RMQ, it depends what kind of game you want to make. If you want a recreational arcadey shooter, then just give them something to shoot, and give them rocket launchers. It's simple and fun. If you want creepiness and a general feel of insecurity, then be unfair, have monsters go invisible, attack from behind without warning, have monsters strafe instead of waiting to be shot, put stress on the player, add in radioactivity / nagging ambience sounds / sepia screen tints and give the player but a rusty pistol.
