I read this article by Michael Hawley called, "Extending Card-Sorting Techniques to Inform the Design of Web Site Hierarchies". In it, he mentions some options to extend and complement traditional card-sorting practices. The one I found most interesting was Focus Group Card Sorting. Basically you find a focus group of 8-15 people and bring them to a physical location and have them do the card sorting exercise online but with you there to listen to and record their comments and discuss their choices.
I'm not sure we'll have the time or resources to do this or even if it will be necessary, but I still think it's a good idea for future card sorts, if nothing else.