How can software be "equipment and method related to the transmission of information" until combined with something to run it on? Maybe the user of the software is infringing, but surely not the provider of the software?
It really bugs me that software developers get chased for patent violations when software by itself doesn't do anything. If every last device that could execute the software were destroyed would it still violate a patent? Many software firms provide indemnity to their users against potential patent violation, but if someone runs a free software project then they explicitly do not.
Backed up the system lately?