Here is a small list of peer reviewed open access journals that I’m aware about (if you know more, let me know!):
PeerJ: They charge a one time only fee and you can publish there for your entire career.
PLOS: probably the best known open access initiative out there, but they charge the publication fees from the authors instead of charging the readers.
The Frontiers family: Frontiers is a open access publisher that follows the recipe of charging authors, but they have the great idea of making the reviewer’s and editor’s name public, so that in every paper, one can see who were the “guilty ones” for allowing that specific paper out.
Doing a small research for “Open access journals” once can find a lot of them (great!), I haven’t had the time to go through all of them in detail, but here is a list:
BioMed central: They work the same way as PLOS, by charging the authors.
SpringerOpen: The open branch of Springer
Wiley Open Acces: The open branch of Wiley
Directory of Open Access Journals: here one can find open access journals through a search engine.
Faculty of 1000: Really thinking outside the box, this publisher has mainly four services (as in 22/01/2014): F1000Prime has a commented selection of papers in biology and medicine, recommended by over 5000 Faculty Members. F1000Trials has a commented selection of published clinical trials. F1000Research is an open access journal, with a post publication peer review system. Papers are published after an in-house editorial check as long as all data used in the paper is also made available. After publication, the paper is peer reviewed (reviewers names are public!) and the revision steps are tracked and indicated. Last but not least, F1000Posters is a repository of posters and slide presentations, making all the effort to put up together a nice presentation/poster less useless, since they will have much more visibility than a conference’s time.
GigaScience: is a general biomedical- life science journal that focuses on big data studies. Interestingly they want to provide the normal manuscript together with a database to host data used to generate the article, tools for data analysis and cluster computing facilities.
Paperity.org – is not a journal, but an open access journal aggregator:
Our ultimate goal is to aggregate 100% of Open Access literature, published in any place around the world, in any field of research
Publons – is a system to help scientists record and track the reviews they made for peer-reviewed journals. Considering that scientists spend a lot of time reviewing articles, it seems like a good idea to track these efforts and give credit to the reviewers