Slate's Jack Shafer notes a history of poorly-sourced stories about Quran desecration going back (on Nexis) to 1983. One of the stories he cites is verified; the others may or may not be accurate.
While Shafer thinks that Newsweek made a major error when "It let its anonymous source predict the contents of a future government document," he also wonders why the magazine wasn't "more skeptical about Quran-desecration charges."
Reviewing the history of these charges, Shafer asks, "Could it be that the Gitmo prisoners lied or exaggerated about the Quran story, pushing forward the most outrageous meme in their inventory, and that their inflated charges percolated up to Newsweek? The Abu Ghraib photos and reports from various U.S. military lock-downs around the world should prepare us for the possibility that U.S. handlers committed such sacrilege. But if the original source of the allegations turns out to be prisoners, we might want to view their charges with the same doubts we apply to any testimonies about prisons from prisoners."
Note: I know Michael Isikoff, one of the Newsweek reporters at the center of this maelstrom. We once worked in the same newsroom (though not together); his investigative work was justly held in high regard. While I'm at it, Jack Shafer is a long-time friend; I've written for him at two publications.