Now that we are striving for order, let's be realistic. Piles happen. After all, if a cluttered desk is a sign of a cluttered mind, then what is an empty desk a sign of?
Piles have their purpose and most people have a general system to seemingly unorganized mountains of paper on their desk. These are the "active" projects, not yet ready to "sleep" in file drawers. Visit the design your life blog to read the post on Piles: Everyone Gets Them.
I especially like Mike Essl's idea in the comment section. He uses clear pockets (called Job Ticket Holders available at Kinkos). If you are not ready to condemn paper or projects to the file drawer, place all related paper in a clear pocket. They are accessible on your desk as a distinct pile, ready to receive your attention. It may be the difference between drowning or keeping afloat!