It doesn't matter that 90,95,99,whatever% of sourceforge projects are dead audio mixers that not even the original developers are using. Those projects can be ignored. They don't take up physical space, and we're not running out of internet. Just ignore them.
What matters is the quality of the actively developed free software. Any study on the quality of FOSS should start and end with actively used and developed software and ignore those that have been selected out of the software pool, because that is the process of FOSS development.
I know I have lots of 'open source' half finished projects, which I may or may not be using, and it doesn't really matter to me if someone else wants to take the code and continue it, or fork it or what have you.
I certainly prefer for my web server an open source stack. That's not to say there is anything wrong with proprietary alternatives, but I worked for a very large company that transitioned from proprietary software to open source, precisely for the 'open source' credo (it's stable, tested, more secure etc) as well as its gigantic cost savings annually.
I think proprietary software has a place, but I would like to see the author argue when and what those cases are instead of just talking shit on free software. Perhaps desktop applications for MacOSX and Windows is such a case...
Free software advocates don't have to fight that particular battle, since software freedom for them is the end, and not a means.
I agree with you about proprietary software, but that model is rarely attacked in the way open source and free software is.
There's plenty of great free, open-source, and proprietary software out there, and many interesting debates to be had about the merits of competing packages. If some pointy-hair insisted on an obtuse argument about how all the crap projects on SourceForge are diluting the power of open source, I would get another job and let him replace me with someone with a higher tolerance for incompetence.
The more important metric is to measure is how good the top 10% (of each) is.