Here's an ancient -- but still relevant -- piece from Tim O'Reilly: "Software and Business Method Patents".
Here's a great article in Slate on the consequences of software patents. "Weapons of Business Destruction: How a tiny little 'patent troll' got BlackBerry in a headlock".
The biggest issue with software patents is always the "non-obvious" issue. Generally, this can be debated, so a prior art review is far more valuable.
See "Peer Review Starts for Software Patent Applications: IEEE Spectrum talks to the founder to Peer-to-Patent Beth Noveck". This is where the rubber hits the road.
To participate, see Peer To Patent. Locate prior art and make patent trolls get real jobs.
Also, see this: "A patent improvement: Intellectual property: A new scheme will solicit comments via the internet to improve the vetting of patent applications".