As I was saying here:
http://www.freesoftwaremagazine.com/blogs/ideas_for_patent_reform

There are three ways of rectifying the software patent problem:
1) Lobbying - demonstrating the law is unethical, if not invidious and impractical.
2) Rendering and demonstrating s/w patents as completely ineffectual and/or redundant.
3) Demonstrating patent restricted s/w has a lower economic return than unrestricted s/w.

1:- Good luck with the lobbying. ;-)

2:- Create a standard s/w configuration infrastructure to rapidly adapt the moment s/w is put on notice for infringement. Demonstrate that patents simply create unnecessary work for the free s/w community to treat as damage to be routed around - inevitably avoiding patent licence revenue by providing both a rapidly deployable non-infringing alternative, and a deferment of licensing fees to the end user (should they insist on use of patented code).

3:- Create a collective funding mechanism to facilitate the commission of free software.