Books
Patent Failure: How Judges, Bureaucrats, and Lawyers Put Innovators at Risk by James E. Bessen and Michael J. Meurer (2008 Princeton University Press) - If you think the patent system is out of sync with the software industry, you need to read this book.
Democratizing Innovation by Eric Von Hippel (2005) - You can download a pdf copy of the book here, or you can go to this link to buy a copy.
Articles
The Private Costs of Patent Litigation by James E. Bessen and Michael J. Meurer (2007, rev. 2008)
Patents, Venture Capital, and Software Start-Ups by Ronald J. Mann and Thomas W. Sager (2007)
Empirical Studies of Innovation in the Knowledge Driven Economy by Bronwyn H. Hall and Jacques Mairesse (2006)
Patent Thickets: Strategic Patenting of Complex Technologies by James E. Bessen (2002, rev. 2006)
Takings, Judicial Takings, and Patent Law by James N. Bunch (Texas Law Review 2005)
The Patent Litigation Explosion by James E. Bessen and Michael J. Meurer (2005)
Do Patents Facilitate Financing in the Software Industry? by Ronald J. Mann (Texas Law Review 2005) - I happen to not agree with Ron's conclusion, but his paper is still a worthwhile read.
An Empirical Look at Software Patents by James E. Bessen and Robert M. Hunt (2004) - This is an early version of the paper. Jim and Bob have published subsequent versions.
The Software Patent Experiment by James E. Bessen and Robert M. Hunt (2004)
Sequential Innovation, Patents, and Imitation by James E. Bessen and Eric Maskin (2000, rev. 2003)
Mark Webbink on Software Patents October 9, 2007
Mark Webbink and Alan Cox on Red Hat's Patent Promise Updated March 17, 2008
Links
Peer-to-Patent Project - The Peer-to-Patent project, run by New York Law School in conjunction with the U.S. Patent and Trademark Office, is designed to improve patent quality by providing third-party experts the opportunity to identify prior art and issues of obviousness during the pendency of patent applications.
Mark Webbink Video on Software Patents (2007)
Research On Innovation - James Bessen's website. Research on Innovation is a non-profit organization created to conduct and promote research on technological innovation and to disseminate the results of this research to a broad audience, both in academia and in industry.
Are Software Patents Evil by Paul Graham (2006)
Intellectual-Property Rights and Wrongs by Joseph E. Stiglitz (2005)