On the December 6, 2006 edition of The Colbert Report, Stephen placed a cardboard box on his Shelves of Honor. He placed it there to remind people, like Gwyneth Paltrow, that they often say things they don't mean.
On the January 4, 2010 edition of The Colbert Report, prior to unveiling the new set for the HD version of The Report, Stephen said goodbye to his old set and some of the props. He specifically singled out the Cardboard Box, saying "I think I'll miss you most of all, Box Containing Gwyneth Paltrow's Head," thereby confirming the box's contents.
During a cursory examination of the new set's shelves Cardboard Box did indeed appear to have been retired.