One scene that I believe many people have commented on, is Kusanagi's battle with the spider tank in Ghost in the Shell.
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That would be one of my favorites, as well. Fantastic animation, and you really start to get a sense of how badly Major wants to meet the puppet master.
Along that same line, episodes 13, 24, and 25 of GITS SAC have some of my favorite gun battle moments in anime or live action.
And seconding other mentions, the opening of Karas has to be my favorite anime battle sequence of all time. It used to be The Marcus Brothers taking on the town full of vampires, but frankly it's hard to compete with something as excellently choreographed as Karas.
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