Peerage of Science
"Basically you submit your paper before to get advice and reviewing from people that is part of the project (free and open),they allow open (not blind) reviewing and submission (we all knew who is the other) , there are journals subscribed that can directly contact you to publish the reviewed version or you can send your work with the reviewing data to another journal that could accept your paper or ask for some more reviewing."
Directory of similar open publishing services
Compiled by Patricia Castillo-Briceno:
Pre-prints submissions for free, post print publication at a fix yearly low rate (compared to other editorials)
- Biomed Central http://www.biomedcentral.com/
Editorial of quite reputed journals in biomedicine, however you have to pay to publish with them (about 2000 USD), but your papers are open access and you keep your rights
Free Access: A Core Principle of PMC ; As an archive, PMC is designed to provide permanent access to all of its content, even as technology evolves and current digital literature formats potentially become obsolete. NLM believes that the best way to ensure the accessibility and viability of digital material over time is through consistent and active use of the archive. For this reason, free access to all of its journal literature is a core principle of PMC. Please note, however, that free access does not mean that there is no copyright protection. As described on our copyright page publishers and individual authors continue to hold copyright on the material in PMC and users must abide by the terms defined by the copyright holder.
- NIH Public Access Policy http://publicaccess.nih.gov/policy.htm
Wellcome trust http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Open-access/Policy/index.htm ; British Heart Foundation http://www.bhf.org.uk/research/research-grants/managing-your-grant/open-access-policy.aspx ; In summary Uk policy encouraging to get public access for all papers from research funded by public sources, so they provide additional funds to get open access when needed.
- Deutsche Forschungsgemeinschaft (German Research Foundation)
http://www.dfg.de/en/research_funding/programmes/infrastructure/lis/funding_opportunities/open_access_publishing/index.html ; Similar policy that UK's above
- Europe PubMed central http://europepmc.org/
Similar to PMC but european
- Gigascience http://www.gigasciencejournal.com/
This is a very interesting journal/initiative, as stated by them they state: "GigaScience aims to revolutionize data dissemination, organization, understanding, and use. An online open-access open-data journal, we publish 'big-data' studies from the entire spectrum of life and biomedical sciences.
To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data and provides data analysis tools and cloud-computing resources."
Maybe the best as a model "pain-free publishing", deserves to be analysed in detail
Open access initiatives compiled with commentary by Xavier Barandaran:
- PLoS (Public Libray of Science)  and Frontiersin
 are the most succesful and innovative of Open Access platforms (almost entire scientific ecosystems). You have to pay to get published there which I think it is a good thing (particularly as long as they maintain the policy of free publishing for developing countries or universities without resources).
There exists an open access journal directory  with statistics.
9,741 Journals 5,649 searchable at Article level 133 Countries 1,627,853 Articles
- The WormBase  and WormBook
http://www.wormbook.org/ is an amazing project, like a super-repository of papers, data, etc. for the study of C. Elegans worm (one the most important animal models, the smallest multicellular organism on Earth). Everything is copyleft and there is an amazing community build around this work and knowledge base. A connected project is http://www.openworm.org/ that tries to simulate the whole life of C. elegans with open source software taking the knowledge-base of wormbase.
Biology is one of the most complex scientific fields nowadays (partly because of the molecular details and the huge amount of data produced by labs, and the very complexity of life). Huge data-sets demand an enormous collaborative effort to produce knowledge out of it, and that demands the establishing of protocols and data-structures and data-query and analysis tools. Big Data commons initiatives like http://bd2k.nih.gov or the resources put available by the European Bioinformatics Institute  are opening the way to new forms of massively collaborative science. An interesting example of open data results is the Open Data Drug Discovery initiative in India http://www.osdd.net/
- For a theoretical analysis of the superiority of open science check out Woelfle, M., Olliaro, P., & Todd, M. H. (2011). Open science is a research accelerator. Nature Chemistry, 3(10), 745?748. doi:10.1038/nchem.1149
- Scholarpedia is a good case study of a peer-reviewed wikipedia style
scientific encyclopedia. http://www.scholarpedia.org
- The Complex Systems Society  is a huge
community-platform that provides innumerable services: data, software, wikis, etc. around complex systems studies, all copyleft and participatory, including the research roadmaps, discussed online and in conferences to push the research agenda. You can also explore the community at http://communityexplorer.org/ (see video: http://vimeo.com/38383946). It will soon open its MOOC as well with open content and lab applets.
- Open repositories are a very important push for science. Arxiv
 is by far the most known, it operates for the fields of fields of physics, mathematics, computer science, quantitative biology, quantitative finance and statistics.
- Citizen-science  and Public Labs
 are project and communities to check as well.
- Not everything is about open access, data, knowledge bases and labs.
Science is the clearest example of State Partnership on the commons nowadays BUT the way in which scientific evaluation and funding is organized is far-beyond a commons-based approach. There are two (or three) traditional modes of financing-organization procedures: a) local university selection processes (prone to mafia-style local constraints, nepotism, etc.) and b) "objetively"-measured standards and state-run selection based on impact factor and other CV-standardized achivements and c) private universities might combine some of the above with other criteria. None of the above guarantees and return to the commons: a) does not guarantee quality and b) only guarantees a pseudo-monopoly based quality measurement (mostly run by Thompson-Reuteurs indexes). It is important to innovate with more fluid scientific funding and organizing modes, including new impact indexes, common's return, participatory and open access result enforcements, etc.