A Reuters article describes one of about 35 software patent suites pending against Microsoft. While Microsoft can defend themselves against these suites that most likely involve poor quality patents, most smaller companies could not. A poor quality patent is a patent that would not stand up to the rigorous tests of useful, novel and unobvious that happens in a court. No matter what the theoretical benefit of the few good quality software patents (it is controversial whether there is benefit), it should be obvious that the bad quality patents are harmful to software innovation.
It is estimated that 60% of software patents granted by the USPTO would not stand up to rigorous novelty tests (prior art searches), and that the number may be as high as 95% failure when the other two tests are carried out. I strongly believe that unless patent quality can be raised up to at least 90% good quality patents in a given subject matter, then no monopolies should be offered at all in that subject matter.