The effects of the Klingon disruptorrip-you-apart-from-the-inside-out-while-you-scream-in-agony beam are... pretty horrific.
The Genesis planet tearing itself apart.
Kruge: Yes, exhilarating, isn't it?
The sheer suddenness of David's death - along with a death rattle that seems to indicate he was stabbed in the throat.
The scene where child!Spock turns into teen!Spock. Bones cracking, skin stretching, and screaming. Lots of screaming. And then, Fridge Horror sets in when you realize thatyou heard that screaming before they came upon child!Spock.
The most graphic depiction of disruptor disintegration Star Trek had ever (up to this point) shown. The victim grabs his head in agony as he falls back against his control console and is consumed by energy from the inside, out.
McCoy under the influence of Spock's katra, when you think about the implications. Especially the scene where Kirk finds him in Spock's quarters.