10 Most Terrifying Video Game Enemies of All Time 

OMG, Otto was terrifying! Although, I REALLY think that Giygus from Earthbound should've been on that list. He's just... "shudders".

I was always SO freaked out by those spiders in Ocarina of Time... *shudder* But I'm arachnophobic, so that probably didn't help. XD

The headcrabs are the best. That iconic scene near the beginning of Half-Life 2 where you had to navigate through that maze past piles of bloody bodies just really creeped me out.

They are, Spuddy... Did you read page 2? I've never played that game before, but they had a video of them on there. WHOA SHIT. Those things are horrifying.

I have to go hide under my bed now...

Oops. Just checked the second page, didn't notice it before. But yeah, they are really weird.

These articles on Cracked seem to focus on NES games and recent PC games. That's fine, but there's a bunch of other games out there, some with some pretty scary villains.

Some others for consideration:
* Mr. Big from N.A.R.C.
It was bad enough that you had to fight the huge fat bloke, but then you shot off his skin in the battle, so that he was a big pulpy mass of muscles and fat which spewed toxic blood at you. Continuing somehow, you manage to strip him down further to a giant skull with rolling eyes and a tongue that would rocket out at you; a French kiss with the undead that meant instant death. Finally, all the fleshly parts would burst, and you were left with a giant skull snapping its teeth at you. Cracked.com has a similar list, of the 10 most impossible games - N.A.R.C. belongs on both lists.

* Type V Demon Lord - Larn
You manage to fight your way down ten levels of insane dungeon. Maybe you've picked up dozens of spells so that you can tiptoe invisibly through the dungeon or disintegrate your opponents with a word, maybe you've equipped regeneration rings for fast healing, rust-proof armor and a globe of invulnerability, maybe you've even bought the lance of death or the sunsword, so that every monster dies with one hit. It doesn't matter. You get down to that bottom level, and you're faced with an enraged, relentless, invisible lord of the nether realms who carves pieces off of you as easy as scooping whipped cream. He's resistant to all magic, goes through protective wards and armor alike with ease, can't be detected with any magic, has some unknown but very high amount of hit points and laughs off your burliest attacks with a wink. You'd be traipsing along, trying to get the Eye of Larn, and suddenly wham! a Type V Demon Lord is there, chomping on you. All you can do is run at that point, and hope that there's a door you can close on the beast, a stairway or a teleport trap in your way. (an aside: the Type of demon lord you encounter is variable in the game, so if you met a less than Type V, you had a chance...but you wouldn't know which it was until it walked up and hit you)

* Jaggi pilots in Rescue on Fractalus
This was primarily a space flight simulator, where you flew a spacecraft at low altitude above a planet's surface to try and rescue other pilots whose ships had been shot down; sort of a realization of "Defender-meets-Terminal Velocity" (I know, I know - TV came much later, but it's really the same sort of gameplay). As you flew, you scanned for the stranded pilots' beacons. Detecting one, you'd follow the beacon past all kinds of flak and laser towers until the crashed ship was in sight. You'd have to survive long enough to successfully land your ship on the rocky surface - close enough to the wreck that the pilot could make it to your ship without getting shot - and watch the pilot run up and under the cockpit. You had to turn off your shields so that the pilot could get to the ship, then wait while he ran up to and then under the ship. After a moment, you'd have to open the hatch when he knocked, to let him in. This went fine for the first few levels, but at some point the alien villains got to the pilot before you, killed him, and put a ringer in his place. The beacon was on, you'd fight you way through, land, and watch the little bugger run up to your ship. You'd wait for the knock, and suddenly with a discordant whine of simulated violins, the Jaggi creature would rise up in front of your cockpit, snarl, and punch through the screen to vent you to the poison atmosphere and eat you alive while you suffocated. After the first time it happened - if your heart withstood the shock - with each rescue you then had several seconds to wait after the pilot ran under the nose of your ship, trying to decide: "Should I turn on the shields and fry one of my friends, or is he actually a monster and is going to eat me alive?" Terrifying. I played this late and night with some friends when we were 12 or 13, and we all screamed like little girls when the Jaggi rose up. After that first time, we must have fried a full score of our downed compatriots, unable to bear the wait for that "knock-knock-knock!"

I looked up this last one, and apparently there was another possibility in the game: you could open the hatch before the pilot reached it, in which case he'd board automatically (no knocking first). If he was a fellow human, you were good. If he was actually a Jaggi, he'd scuttle your ship from the inside.

"scuttle your ship from the inside"

For some reason, this phrase, in reference to alien invaders boarding your aircraft to annihilate you, totally made me LOL :D

Great addition to the Cracked article, Harold! Those baddies definitely seem like they would've been good inclusions.