The Information High sequence, the "Dog Fight" sequence between Guld and Isamu (named for the music that plays over their battle) and Guld's duel against the Ghost X-9. Basically, the whole last OVA/30 minutes of the movie is one long moment of awesome.
Also one for the intro. Absolutely no words are in it and, really, it doesn't need any. The sheer simplicity of it is awesome in an artistic sense.