In a Federal Reserve Bank of Philadelphia working paper, James Bessen (Research on Innovation and Boston University) and Robert M. Hunt (Federal Reserve Bank of Philadelphia) find that software patents do not lead to an increase in software inventions: An Empirical Look at Software Patents
The authors found that during the 1990s, all else equal, firms who increased their focus on software patents tended to reduce their R&D intensity relative to their peers. This suggests that in the 1990s, software patents substituted for R&D. This negative relationship was found only in certain industries, specifically those industries noted strategic patenting.
Full Text (pdf): An Empirical Look at Software Patents (Mar. 2004). See also the less technical The Software Patent Experiment from the same authors.
