I will admit to jumping several times while playing Bioshock 1 and 2.
Well, there are a few WoW bosses where if you don’t jump you will die (Hodir, that Nexus dragon)… or is that not what you meant?
Dead Space has good make-you-jump monsters.
They come from the floors and celings so quite often you can be in a room and one will be RIGHT behind you without you noticing (until it attacks or you turn around)
Very good game apart from the fact that (on the PC) I was unable to re-map the directional controls to the arrow keys, and it had the ‘acceleration’ turned on, so aiming with a mouse was quite frustrating (small movements with the mouse did nothing to the cursor, until the physical movements were fast enough to trigger movement, then the movement would be too fast)
Maybe it was just my age at the time, but the 3D Mario game for N64 had one level where there was this giant eel lurking in a sunken ship that you had to lure out and then get evade so that you could get into the ship. For whatever reason that eel just sitting there lurking until you get too close stuck in my mind as being really eerie.
Many years later I went Scuba diving on a similar looking wreck. I peaked into the cabin and there was a giant grouper sitting in a similar position staring out at me. Nearly spit out my regulator.
Just last night I was cruising through Old Olney in Fallout 3…you know, the town overrun by Deathclaws? Most of the time you can spot them from a distance and severely wound them before they get to you, but down in the sewers…I’m glad I was packing my shotgun, because when I turned a corner and got a faceful of ugly bastard with claws, my panicked firing still managed to hit it.
Bioshock.
A large empty warehouse room, with a couple of plaster figures. All is quiet. Look around a bit and then notice “hmm…I thought they were closer to the wall…and weren’t there only two figures, now there are three…” Oh well, keep looking in corners, then turn back around…
“No, I’m sure they moved this time, I swear one of them was past that column…I’ll do a quick pivot and check…”
I turn away and face the wall, then turn back around, and AAAIIGHGHH! There’s a freakin’ splicer jumping right at me. I scream and hurl the controller at the ceiling and nearly break my foot on the coffee table.
EXODUS was billed as the spawn of two evil magi, who between them were responsible for all the ills of the world several times over.
Then when I finally reached that thing, it looked nothing like any other creature in the game. It was something that could only have come from the twisted mind of an Apple ][ Assembly programmer.
small aliens in Alien Vs Predator. It was a long while back, but I distinctly remember them jumping out from behind, ontop, around, underneath… anywhere but where you expect them to be. And the game changed it every time, so no reload and light on moments. Add in the radar with the increasingly faster proximity beeping from the movies - and I was one petrified kid.
Bioshock got me plenty.
I was going to say this.
I mean, there are lots of Diablo (I & II) monsters that are harder or more likely to kill you, so scary in some intellectual sense, but there’s definitely something about the Butcher that gets your heart pumping and nerves sparking.
I’m still freaked out by Stauf in the 7th Guest, especially him in the labyrinth.
“You shouldn’t have turned down here!”
Mine seem tame in comparison.
Then again, they probably come from a younger Demographic. As was the case for me, when I played them
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Commander Keen** : Not so much the monsters, but the “death” music cue. Especially going over multiple spikes. I think the Dopefish actually made me jump the first time I saw it. You don’t expect something that big there.
Number Munchers : this one, I know is the music. You go along munching your numbers, and then the cue for the troggle occurs. No warning.
Argh! Especially if you’re playing late at night, headphones on, all is quiet, and then you nearly jump out of your chair when he says something.
The Haunts are creepy, but what got to me first was the zombies. The first time I encountered one in The Dark Project, I managed to eventually beat it down. After exploring the area for a bit, I came back through the hall where I left it, moving quickly because I figured it was safe. I didn’t know the damn things could get back up after being “killed”. I was right on top of it when it let out one of those creeptastic groans and stood up. Yeah, I jumped.
Bioshock provided a lot of jumps. The level designers were very good at getting into a player’s head and laying out set-pieces with splicers.
Wow, that’s a good one. I had forgotten about that, but that definitely brings back fond memories.
I came in to post another one from that game. Remember when you encounter your first “Licker”? Right beforehand, you’re walking down a hallway, and you suddenly catch a glimpse of something big and evil-looking scamper by the window right next to you. I about wet myself the first time I played through that.
Bioshock again, dentists office, totally empty, goodies on the dentist chair, I go and get them, turn around and there is a splicer in a medical mask right behind me, just standing there, staring. I killed him before he did any damage, but damn he freaked me right the hell out.
The sole purpose of that guy is to scare you. He won’t attack until you do. And yes, it’s a cheap but extremely effective scare 
I need to get around to finishing *Bioshock *one of these days. It really is such an excellent game.
Too many startling things there to get specific, so I’ll sum up by saying that I’ve been frightened by the sound of *my own footsteps *playing that game. 
Along those lines: the Kronos Class Titan in City of Heroes. I wasn’t aware this Giant Monster would ambush after completing a certain story arc so I was like, “What’s this? An earthquake?” Then I saw it! And started running; it followed. I put out a broadcast “Hey, can anyone get this Titan off my ass?”
The original AvP was great for this. I loved the way the aliens made little clicky noises, so you could hear when they were coming, EXCEPT FOR WHEN THEY DIDN’T ARGH!!! The way they changed location on subsequent plays was a great idea, and something that surprisingly few games seem to do.
Also, I’d like to add the head spider things, and the demonic babies from Doom3. I’ve played that game through several times, but I hate the levels where those things appear. They aren’t even particularly tough to kill, I just don’t like looking at them.