No. 5: Beheading by The Chainsaw (Resident Evil 4)
Why? This few second scenes of The Chainsaw beheads the player which act as Leon. The scene of Leon's head being separated with his body really makes the player stuttered. Maybe after several times, you will get used to it but still, it will give you a moment of shock when watching it.
No 4: Limbs Cut by Robot (Call of Duty: Black Ops 3)
Why? In this game where the player is battling an army of robots, there is a scene where the robots have captured you and the next thing you know is your limb are being cut one by one. The fact that make me horrified by this scene is that the robot does not have any feeling so it would feel nothing when cutting off any part of your body. With the scream and blood, owhh it will really give you a horrify moment with this scene!
No. 3: Beheading of Helios (God of War 3)
Why? Well beheading itself is a brutal thing to do but this one is done with BARE HANDS! Yes literally bare hands! Kratos pulled out Helios's head with his bare hand. I don't know about other people but beheading itself is one thing while beheading with bare hands is another thing. Try to imagine if it happens in real life and you'll realize how brutal it is.