I do like the music of the PT a lot, even if it never feels as groundbreaking as that of the OT.
Apart from the cues mentioned by DavidBrennan, I do think "Padme's Ruminations" and the Order 66 lament (I'm not sure what track on the released CD this belongs to - is it "Anakin's Betrayal"?) rank as some of the best pieces of the whole saga.
In fact, the Order 66-scene is the only scene from the PT that actually moves me, to the point where I might even shed a tear or two. Even if George's direction and editing during that scene are uncharacteristically brilliant, I've narrowed the reason for this down to the score. It's an incredibly emotional piece of music, and that's what John Williams does at his very best. Makes me sad over the deaths of the most two-dimensional of characters. If only there had been more pieces like that in the PT.