No spoilers here...for me at least, the entire fifth episode of FLCL, but namely the fight Haruko has with the giant gun-toting monster thing. I think it was the combination of the music and action in those scenes that really just defined the entire series, and I'll always think of that as one of my all-time favorite parts of any anime.
Ok, I lied, spoilers for Eva:
Oh, and for good measure, pretty much all of Beyond the Clouds was memorable for the animation alone.