I love this scene from Death Note. I like it when one's elaborate plan finally comes to fruition, and this "just as planned" scene was great for that.
And this scene from episode 13 of Paranoia Agent. When detective Keiichi Ikari comes to term with reality and decides to abandon his delusion. Very cathartic moment.
Oh, for a third, I guess I enjoyed Future Diary's introduction to the killing game with all of the different participants, that was fun; though I mostly want to make note of it rather than it actually being one of the most powerful for me.