Here's some quotes that might be relevant:
"All of the empirical work in this area has come basically to the same conclusion--that patents are a particularly important inducement to invention in only a few industries. In pharmaceuticals, for example, patents seem to be an important part of the inducement for R&D. However, in industries like semiconductors and computers, the advantages that come with a head start--including setting up production, sales and service structures, and moving down the learning curve--were judged much more effective than patents as an inducement to R&D." (ABA, 2007, p. 108)
"[P]atents are much less important as a means by which most software firms—the majority of which hold no patents—capture competitive advantage from their innovations." (Graham, 2009, p. 1262)
"This report examines changes in the patenting behavior of the software industry since the 1990s. It finds that most software firms still do not patent, most software patents are obtained by a few large firms in the software industry or in other industries, and the risk of litigation from software patents continues to increase dramatically. Given these findings, it is hard to conclude that software patents have provided a net social benefit in the software industry." (Bessen, 2011, p. 1)
"But reforms may yield unintended consequences. In its simplest form, this concern translates into wariness about Trojan hourses: provisions brought into the law by the rhetorical tug of 'competitiveness' and 'intellectual property' may harbor instruments of protectionism and price fixing." (Levin, 1987, p. 6)
American Bar Association Section of Antitrust Law (2007) Intellectual Property and Antitrust Handbook.
Bessen, James E. (2011) A Generation of Software Patents. Boston Univ. School of Law, Law and Economics Research Paper No. 11-31; Berkman Center Research Publication No. 2011-04.
Graham, Stuart J. H.; Merges, Robert P.; Samuelson, Pam; Sichelman, Ted (2009) High Technology Entrepreneurs and the Patent System: Results of the 2008 Berkeley Patent Survey.
Levin, Richard C.; Klevorick, Alvin K.; Nelson, Richard R.; Winder, Sidney G. (1987) Appropriating the Returns from Industrial R&D. Brookings Papers on Economic Activity, pp 783-831.
[EDIT: Just found this on wikipedia:
According to James Bessen, the costs of patent litigation exceed their investment value in all industries except chemistry and pharmaceuticals. For example, in the software industry, litigation costs are twice the investment value.
According to James Bessen, elimination of the patent system would increase the incentives for innovation in all industries except chemistry and pharmaceuticals by eliminating startup litigation costs. (Bessen, 2008)
Bessen, James (2008) The value of U.S. patents by owner and patent characteristics. Research Policy, Elsevier, vol. 37(5), pages 932-945, June.
[EDIT: another good reference:
Bessen, James & Meurer, Michael J. (2008) Patent Failure. Princeton University Press. <http://press.princeton.edu/chapters/s8634.pdf>