Some good news for the Open Acess-movement in general, and for those who have published in PLoS one in particular, particularly Tom Gosden and Fabrice Eroukhmanoff (alongside with me): PLoS ONE will now be listed in Web of Science, meaning that your articles, as well as all future articles in this journal, will now be searchable and appear in ISI:s databases. This is very good news, as the lack of inclusion by PLoS ONE in ISI has been somewhat negative when trying to convince people to publish there: scientists are quite conservative and hesitant to publish if they are not absolutely confident that their papers will be read widely and cited.
It does not matter to argue, in my experience, that Web of Science, is not the only database and not necessarily the best or most inclusive one. PubMed, for instance, is much faster and better, and Scopus covers many more journals than WoS. Many scientists do not seem aware of the fact that these search engines and data-bases are commercially driven, and thus not driven and organized by scientists, with the primary goal of helping scientists. Thompson/ISI simply happen to be one of the oldest data-bases, and the one which claims credit for the term "Impact Factor"(IF), and very questionable measure of journal impact which has recently been criticized by many.
Putting these issues against IF aside for a moment, PLoS ONE will, as a side-effect, soon also get its first IF, since it was needed to be included in ISI before that was possible. It will of course also be interesting to see which IF PLoS ONE will get, although I would not primarily use that as the only or most important criterion where to publish. It is interesting that it took three years before ISI accepted to include PLoS ONE in their data-bases, given that there are many low-impact journals like Odonatologica which has long been included in ISI.
I suspect, although I do not have any proof for this, that ISI are nervous for the new publication model that PLoS ONE advocates, where perceived impact and "novelty" is played down and there is more emphasis on technical quality. In the end, this might hurt the commercial interests of ISI if scientists start to increasingly become more critical to journal-level IF:s (rightly so!). In a better future, there will hopefully be more emphasis on scientific content and article-level metrics of authors, rather than on journal-level metrics, which largely belongs to the pre-internet era and sends out a message that journals like (say) Evolution or American Naturalist are not as important as we, in the field of evolutionary biology, generally think that they are.