One of the best tools I've found for card sort experiments seems to be websort, mainly because you can just send out a link for participants to go through the exercise at their own convenience.
However, at the end of the day this method just returns limited quantitative data, and prevents the researcher from exploring another entirely separate dimension of information. I've never actually performed a card sort, so I don't know if performing the experiment in person is really worth the time. But at the end of other types of research sessions, I like to get inside the participant's head.
Have you found that gathering qualitative data from card sort experiments is worth the time? Based on the nature of card sorting, I expect this would generally need to be more involved than a few follow-up questions that could be included in a non-proctored experiment.
Edit: For the bounty, I'm looking for a why-or-why-not response. If you feel that qualitative data is important, bonus points for specifying what type of information should be gathered and/or which questions should be asked.