The Software Freedom Law Center has now filed its brief in Bilski. It raises three major points: 1) software is just algorithms for computers in human readable terms, and algorithms are not patentable; 2) excluding software from patentable subject matter encourages innovation in software; and 3) the First Amendment prohibits permitting the patenting of abstract ideas. I think you'll find that last point the most interesting.
Fantastic analysis of the amicus brief filed by the Software Freedom Law Center. It's going to be VERY interesting to see where this goes. You can read more on the Free Software Foundation's site: http://www.fsf.org/news/bilski-supreme-court-brief