And things like compression algorithm are patented, and that's very likely skype is using some of it. Reminds me of a project by Intel of providing an implementation of g729 (a voice codec). The source was available, but it was "non commercial usage only" because of the patents mostly.
An interesting project, but doubt we'll see any usable implementation anytime soon IMO. And even if it does, skype will probably alter a bit the protocol to make it fail if it reaches a critical mass.
And Skype can't really easily alter the protocol because of all sort of skype-compatible devices (IP phones and so on).