Another in flight WIFI service is available and the New York Times is reporting that it is not allowing Skype calls:
http://www.nytimes.com/2008/09/14/business/14essay.html
I don't see this as a big deal though it's not clear to me why they'd care much. Perhaps a security issue because it's easier to screen text such that TSA could identify suspicious activity more easily using automated routines at the ISP level.
In any case this is a great boon to business travelers who now can have uptime throughout the flight, especially at the critical time right before and after key meetings and conferences.
