Martha Stewart is apparently an advocate of the clean desk system. Reportedly there are new rules in the new offices of Martha Stewart Living Omnimedia. I think the rules are excessive and counter-productive, especially in what is supposed to be a hyper-creative environment. The pictures make it look sterile and the one worker pictured doesn't look very happy.
Another high-profile fan of the clean desk is reportedly Bernie Madoff, the financier charged in the biggest stock swindle in US history. A New York Times article notes, "The décor in his firm’s New York and London offices was stark. Black, white and gray — or “icily cold modern,” as one frequent visitor to the New York operation described it." At the bottom of the third page of the article are reports of his obsession with cleanliness and his office manager is quoted as saying "you never left paper on your desk — ever."
So for yourself and your office, set standards and policies that support your business goals, but remember to leave enough latitude that workers can be productive.

