It's only April, but far and away the early leader in the unofficial voting for the country's worst supply chain of 2009 is Peanut Corp. of America. Every revelation about this company's operations is an embarrassment. As this USA Today article explains, PCA's supply chain is the poster child for everything that's gone wrong with the food safety system in the country.
But then again, reading between the lines, this article also provides plenty of compelling reasons why the U.S. Government's Food & Drug Administration places a very close second to PCA for the designation of the worst supply chain in America. If you check out the timeline on the whole PCA debacle, it becomes clear it's not even a matter of which party is in the White House or which party controls Congress -- the FDA's policies of looking the other way when it comes to PCA date back to the Clinton Administration, and apparently they kept looking elsewhere during the GWB years.
In short, this is a systemic mess.
That being said, there could be other, equally worthy choices for the title of the country's worst supply chain. Feel free to nominate any company you feel out-performs PCA in their application of worst practices.