I don't remember many, but this creeped me out

Meeting the Chaser in Parasite Eve 2

The last guy, of course.

glitches from any game... 

I can't honestly choose among these:

· Pietoast already mentioned MGS3 crotch-grabbing. Under that premise, we can also include MGS2 crotch grabbing, too:

· Your boss getting steamrolled by an evil train in Killer is Dead. It was difficult to find this scene, but I just pinpointed in this youtube link:

https://youtu.be/FpdmMs_Jvow?t=20m40s

· A lot of scenes in Spec Ops: The Line. White phosphorous, like many others, caused a WTF impression on me.

(Heavy spoiler, do not watch that scene if you haven't played the game)

· Vashyron, in Resonance of Fate, dancing at the sight of boobs.

https://www.youtube.com/watch?v=tVibNKrp8sQ  (Nolan North voices him, btw)

· The villain plot twist in Dead Rising 2: Off the Record. You know, this is a very good WTF moment, especially because everything else is literally the same as in Dead Rising 2. By the time the villain shows up, though, Capcom had the balls to change him entirely and thus surprise people for the second time, which made things all the more entertaining by the way. I wasn't expecting it, and it was a big WTF moment.

· While Far Cry 4 did it first (in a modern context, secret/alternative endings have been around ever since gaming was invented), it wasn't as shocking as the the alternative one in The Evil Within, which caught me off-guards and was a big WTF altogether.

https://www.youtube.com/watch?v=GWdqxN9sQ5g (light spoilers ahead)

· Pyramid head raping a mannequin. That was disturbing moment in my childhood.

· Also, the interactive sex-sequence in Fahrenheit (The Indigo Prophecy in America, but this sequence was not present on the NTCS versions). Considering how shy I was when I was younger, (let's say around 12-13 years old), it was a total WTF moment when you could take your ex-girlfriend to the bed and press the analog sticks to "thrust" her while completely naked, kissing on the bed. I couldn't help but keep pressing the analog stick and thinking to myself "is this really happening?!"

Here's the full sequence, with the (NSFW, duh) scene included: https://www.youtube.com/watch?v=EafNYw7US4U

I can probably think of more WTF moments in my gaming career, but these are the ones that stick out the most. Can't choose, sorry. :P

That...was amazing.

That game was messed up at times. The moment when that guy is coming towards you and basically teleporting contantly... freaked me out.

The ending of Monkey Island 2.

So I'm playing Fallout 3, right? And you know how you can't kill children in that game? Everyone else, yes, children, no. They're bloody immortal.

I don't even remember how it happened, really, but I'm on that ship-city, and there is this brat, this little asshole with a rebellious attitude. I think I tried to talk with him, cause I'm supposed to straighten him out or something, but instead accidentally failed a pickpocket attempt. He goes nuts, of course, starts punching me, and I just back away.

That's when things get interesting. Since I'm not the one being aggressive, another NPC comes over and starts punching the kid. It's hilarious, so I just watch. It's the waitress--wait, is she his mom? Anyway, he starts punching back and it turns into a brawl. The other NPC vendors come over and start attacking the kid. And he's killing them all! The security detail wanders by, attacks him, and they die one by one.

I'm watching a kid wipe out the market district of the ship.

After that, it's down to me, so I make a run for it. The little jerk follows me outside, though, where he runs into a patrol from the Brotherhood of Steel--and he wipes them out, too. I try to pull him into a group of Super Mutants but, unfortunately, he just runs back to the ship. I guess he just likes wasting humans.

It was a very interesting experience. I'm supposed to set him on the straight and narrow but instead I turn him into the Terminator.

The tokyo tower end (Drakengard).

Even the developpment team didn't agree whether it was retarded or genius. After a few years, a spin off and dozens of pop culture reference, I'd say it was genius.