Of *course* it makes a difference.
It shows that you actually give a damn, taking the time to thank someone for talking with you and gives you yet another opportunity to reiterate how much you want to work for their company.
The flip side to the argument is this: the upside of a thank-you card is it gets your name in front of a recruiter (again) and could move your resume to a short stack..the downside is that it might be a waste of your time? Given the cost and effort involved with attending a job fair, that seems like a pretty favorable risk/reward proposition to me.