Card sorting is a popular usability activity to help determine intuitive menu structures. There are several options for doing a card sort on a computer but for one reason or another I haven’t been satisfied with any of them (too expensive, too limited, too buggy). When I need to do a card sort, I still use an old and buggy (but free) program from 2001 (IBM’s now discontinued Usort and EZcalc).
Finally, there is a new application for affinity diagramming (conceptually similar to card sorting): StickySorter from the people who make Microsoft Office (Office Labs). It looks like the developers are looking for active feedback. I haven’t played with it extensively yet but one thing missing seems to be any way to analyze the data (which IBM’s application does).