I'll second what cruiseluv says about going in the afternoon. We hired Claudio's limo service for a tour of Rome, and Claudio took us to the Vatican in the afternoon to miss the lines --- and we encountered none. Our tour took us past the Vatican entrance in the AM and the lines were bad! The reason for this, I think, is that the Vatican presents a case of "sensory overload" wherein to REALLY see it it would take at least a full day --- if not two. When you go in the PM, all you get is sort of a "sampling" of what is there.

Thanks,
Richard