I will add one more thing to my list. The scene during the final battle when the giant droid carriers park in front of the Gungans, and when the battle droids all activate at once and start marching on them. I know everything after that was pretty terrible, but come on, that was awesome.
This version's been cut up by whoever uploaded it, but you get the idea: http://www.youtube.com/watch?v=p6R9UkpyvSM#t=2m10s