However, not all researchers have completely embraced OA journals. There are two commonly articulated concerns. The first is that many OA journals are not indexed, in most notably Thomson Reuters Web of Knowledge, meaning that a paper will not show up in topic searches, nor will citations be tracked. I for one do not like the idea of a company determining which journals deserve inclusion, thus affecting our choice of journals to submit to.
The second concern is that some OA journals are expensive to publish in. This is especially true for the more prestigious OA journals. Even though such OA journals often provide cash-strapped authors the ability to request a cost deferment, the perception is that you generally need to allocate significant funds for publishing in OA journals. While this cost may be justifiable to an author for inclusion in a journal like PLoS Biology, because of the level of readership and visibility. However, there are other, new, profit-driven journals, which see the OA model as a good business model, with little overhead and the opportunity to charge $1000-2000 per article.
I think that, with the rise of Google Scholar, and tools to assess impact factors (e.g., Publish or Perish), assessing difference sources for articles is available. The second concern is a little more serious, and a broad-scale solution is not readily apparent.
Number of Open Access journals
Regardless, OA journals have proliferated in the past decade. Using the directory of biology OA journals, I show above that the majority of OA journals have appeared after 2000. Some of these have not been successful having faltered after a few volumes, such as the World Wide Web Journal of Biology which published nine volumes with the last in 2004. I am fairly confident that not all these journals could possibly be successful, but I hope that enough are. By having real OA options, especially higher-profile journals, research and academia benefit as a whole.
Which journals become higher profile and viewed as an attractive place to submit a paper is a complex process depending on a strong and dedicated editorial staff and emergent property of the articles submitted. I hope that researchers out there really consider OA journals as a venue for some of their papers and become part of the 'win-win' equation.