The five best peices from the whole SW trilogy soundtracks (so far) for me have been Duel of the Fates, Vader Theme, Battle in the Snow, The Trade Federation theme, and funeral pyre music.
I like the Trade Federation theme SO much because it brings me back to when i was in middle school and first bought that ST, i loved it. Also, Duel of the Fates was my first real introduction to cool epic orchestral/choir music like that. It makes everything seem so damn awesome. Now i notice it in every movie its in and realize that it is very effective at making things dramatic.
In AotC, i was basically filled with some sort of awesome emotion when the Imperial March played right at the end when it showed the ships and clones and Palpatine. It was like at that moment the calm before the storm ended. Cool.