So I've personally sworn off of Software Patents. The stated goal of a patent system is to foster innovation. The concept being that if a person or entity can be guaranteed a limited monopoly on their innovations, they are more likely to invest the time/money to innovate.
I get this, and I think it makes sense, or at least it does for certain markets. However, the online world is one where interoperability is key. In fact, the major feature of the internet is a common set of standards that are used to communicate between different operating systems, clients, and tools. One reason we can't 'fix' email SPAM is that the world has agreed on a standard (SMTP) and implemented it over and over again. HTTP, FTP, etc. These have been around forever, have been implemented tons of times, and these open and agreed upon standards have enabled the amazing growth we've seen.
I had a recent discussion with a friend familiar with Samba and SMB/CIFS. While I am not an expert on the topic, the general goal of Samba appears to be to facilitate the ability for Open Source software to be able to interoperate with windows clients and servers by reverse engineering the client and server code written by Microsoft. This is a classic example of an effort that may violate Microsoft's Software Patents, but provides greater interoperability for people who want (or need to) to run mixed environments. It also allows them to avoid paying licensing fees to Microsoft.
While I will conceded that based on our current laws and regulations, the Samba folks may be violating Microsoft's Software Patents, I would vigorously argue that the system is wrong. There is no real need to have these patents, and the goal of protecting innovation is simply not a valuable return for the immense costs necessary to maintain and enforce them.
What I find more than slightly amusing is the current situation Microsoft faces regarding Software Patents. As the Cory Doctrow's post explains (certainly not a Microsoft fan, so take it for what it is worth), and the underlying Groklaw post explains, the changes for the GPL 3 license and Microsoft's previous dealings with Novell may have put Microsoft in a position where they now must license their Software Patents to all Linux users. Now, this is very much NOT an open and shut case, but the fact that no one is really confident about the situation is a concern by itself.
While I do find this amusing, I actually sympathize for Microsoft and see this as yet another example of the absurdity of the system we are now in. If Microsoft, with its cadre of lawyers can be trapped in a situation like this, than how can Joe on the street have any hope of leveraging this system to protect his innovation? How can anyone claim this system is helpful to anyone but the massive players (IBM, Microsoft, etc), and that simply isn't what America is (should be?) about.
Now, there is a big difference between a software patent and copyright. I firmly support the existing copyright law. It should not be legal to steal, or decompile and reuse, software that is not explicitly licensed to allow that.