One thing that's difficult to measure but probably not trivial is the overall cooling effect. What I mean is that the tangible cases in which patents really ran into conflict don't indicate the number of cases in which technologies were never researched to begin with because of the risk of infringing a patent.
The cooling effect probably isn't significant for the mythical basement hacker who does it for love, but decisions about what research to pursue are made all the time in larger companies, and one of the factors is potential for legal trouble.
This is an excellent point. Basically the patent minefield concept. The insanity of software patents has created an overall sense of fear. There is no way to quantify this aspect of patents' negative effect on progress.
The cooling effect probably isn't significant for the mythical basement hacker who does it for love, but decisions about what research to pursue are made all the time in larger companies, and one of the factors is potential for legal trouble.