Bo-Christer Björk, Annikki Roos and Mari Lauri have published "Scientific Journal Publishing: Yearly Volume and Open Access Availability" in the latest issue of Information Research.
Here's an excerpt from the abstract:
Results. We estimate that in 2006 the total number of articles published was approximately 1,350,000. Of this number 4.6% became immediately openly available and an additional 3.5% after an embargo period of, typically, one year. Furthermore, usable copies of 11.3% could be found in subject-specific or institutional repositories or on the home pages of the authors.