From an 2002 New Yorker Essay from Edward Tufte: 

Paper enables a certain kind of thinking. Picture,for instance, the top of your desk. Chances are that you have akeyboard and a computer screen off to one side, and a clear spaceroughly eighteen inches square in front of your chair. What covers therest of the desktop is probably piles—piles of papers, journals,magazines, binders, postcards, videotapes, and all the other artifactsof the knowledge economy. The piles look like a mess, but they aren't.When a group at Apple Computer studied piling behavior several yearsago, they found that even the most disorderly piles usually makeperfect sense to the piler, and that office workers could hold forth ingreat detail about the precise history and meaning of their piles. Thepile closest to the cleared, eighteen-inch-square working area, forexample, generally represents the most urgent business, and within thatpile the most important document of all is likely to be at the top.Piles are living, breathing archives. Over time, they get broken downand resorted, sometimes chronologically and sometimes thematically andsometimes chronologically and thematically; clues about certaindocuments may be physically embedded in the file by, say, stacking acertain piece of paper at an angle or inserting dividers into the stack.

But why do we pile documents instead of filing them? Because pilesrepresent the process of active, ongoing thinking. The psychologistAlison Kidd, whose research Sellen and Harper refer to extensively,argues that "knowledge workers" use the physical space of the desktopto hold "ideas which they cannot yet categorize or even decide how theymight use." The messy desk is not necessarily a sign ofdisorganization. It may be a sign of complexity: those who deal withmany unresolved ideas simultaneously cannot sort and file the papers ontheir desks, because they haven't yet sorted and filed the ideas intheir head. Kidd writes that many of the people she talked to use thepapers on their desks as contextual cues to "recover a complex set ofthreads without difficulty and delay" when they come in on a Mondaymorning, or after their work has been interrupted by a phone call. Whatwe see when we look at the piles on our desks is, in a sense, thecontents of our brains.

Ah, now I know the piles are there for a perfectly good reason.  Thanks to Stephen O'Flynn for the tip.