The Way Things Are Supposed to Work
A short article on MyTreo.net shows a little about how software patents can be effectively used in business.
A lawsuit is filed, the parties negotiate a license, and they agree in some fashion to work together in the future.
I do not mean to paint too rosy a picture on it, but companies or organizations who have at least some software patents (like the OSS developers could have) have a big chip with which to negotiate and conduct their business.