A recent article in PLoS One presents an analysis of the percentage of articles available open access in 2009.
Entitled 'Open Access to the Scientific Journal Literature: Situation 2009' the paper used a random sample of 1837 articles to determine the percentage that are available OA either on the journal site or within a repository.
The findings show that the greatest percentage of OA articles on journal sites are from the biomedical areas (c.13% of articles) and the lowest percentage in physics and astronomy (c.3%).
However the percentage available in repositories showed a quite different spread. The lowest number available in repositories was in the biomedical subjects (ranging from 4.6-7.8%) and the highest was in the earth sciences area (25.9%).
Chemistry showed the lowest total OA availability (13% total).
Of articles published in 2008, they found an average 8.5% freely available at the publishers' sites plus an additional 11.9% that could be found using search engines, making the average overall OA percentage 20.4%.
It should be noted that since they looked at articles published prior to 2009 the results will not reflect the mandate enforced by the NIH at the start of 2008 – it is likely that a similar study of articles published in 2009 and 2010 (including those for whom 12-month embargoes will have expired) will be far larger in the biomedical arena.