I've never had a tremendous amount of success integrating the findings of card sorts into ongoing developments, but have come across one or two services that have been great to use.
Optimal sort is an online service which enables remote card sorts. When I used it I had students sat in a lab during an open day taking part. I never had to help any of them complete the activity, so I guess it would have worked just as well if I'd never met them.
The demo gives a good flavour of what your participants might encounter.
Optimal sort online card sorting
I've also done good old fashioned card sorts with a big pile of printed cards and almost as many elastic bands. One of the reasons I'm not awfully keen on this methodology is the pain of processing and analysing and reporting. However, Donna Spencer's spreadsheet and associated resources make it pretty much as easy as possible.
Donna Spencer's card sort analysis spreadsheet
I think I much prefer designing a website structure and labelling as far as possible, and then testing it. So going down the diagnostic route rather than the generative.
I've previously written about my approach, and a few helpful resources -
First click is vital (blog post from November 2011)