In order to come up with a system to use on the wiki we have looked at a few other journals to see what their policies are. We have picked several journals from the fields that we figure are likely to be covered on this wiki.
Copernicus publications (Open Access publisher) has a Public Peer-Review process described here.
To foster scientific discussion and to enhance the effectiveness and transparency of scientific quality assurance, Copernicus Publications started in 2001 with an innovative two-stage publication process containing the Public Peer-Review. These interactive journals comprise of the fully peer-reviewed journal itself and an access-reviewed discussion forum.
In the first stage, manuscripts that pass a rapid access-review are immediately typeset and published in the discussion forum in an onscreen format. They are then subject to Interactive Public Discussion, during which the referees' comments (anonymous or attributed), additional short comments by other members of the scientific community (attributed) and the authors' replies are published.
In the second stage, the peer-review process is completed and, if accepted, the final revised papers are published in the journal. To ensure publication precedence for authors, and to provide a lasting record of scientific discussions, the discussion forum and the journal are both ISSN-registered, permanently archived and fully citable.
Journal of Plankton Research (JPR) - http://www.oxfordjournals.org/our_journals/plankt/for_authors/review_process.html this is an Oxford publication
Antarctic Science - this is a Cambridge publication, have not been able to find any info on the Cambridge Press website about the details for their peer review process. Although they do offer a service for helping you to develop a peer review process for your own journal/publication.
Guidelines for reviewers of Marine & Freshwater Research
PLoS ONE provides details for reviewers and information on their publication criteria.
From the ICMJE guidelines (http://www.icmje.org/ethical_3peer.html):
Unbiased, independent, critical assessment is an intrinsic part of all scholarly work, including the scientific process. Peer review is the critical assessment of manuscripts submitted to journals by experts who are not part of the editorial staff. Peer review can therefore be viewed as an important extension of the scientific process. Although its actual value has been little studied and is widely debated (4), peer review helps editors decide which manuscripts are suitable for their journals and helps authors and editors to improve the quality of reporting. A peer-reviewed journal submits most of its published research articles for outside review. The number and kinds of manuscripts sent for review, the number of reviewers, the reviewing procedures, and the use made of the reviewers’ opinions may vary. In the interests of transparency, each journal should publicly disclose its policies and average turn-around times in its Instructions to Authors.
Elsevier has a good flowchart for the peer review process here.
Prometheus wiki review disclaimer (at the bottom of their 'gold leaf' standardised protocols):
"This protocol was designated a ‘Gold Standard Protocol’ as it was deemed by the PrometheusWiki Editorial Board to have received sufficient attention (editing, positive feedback, or usage) to have achieved community approval as an accepted standard. PrometheusWiki is not uniformly peer reviewed thus all information read here is without any implied warranty of fitness for any purpose or use whatsoever. ''None of the contributors, sponsors, administrators, or anyone else connected with PrometheusWiki in any way whatsoever can be responsible for the appearance of any inaccurate or libelous information or for your use of the information contained in or linked from these web pages.''
The Promethus wiki is not 'peer reviewed' as such (i.e. the page isn't sent off to someone for review) - it is an approval process determined by the engagement of the wiki "community" - this appears to be solely based on the use of the wiki and is a bit different to what I understand the review process of SOKI to be (idealistically).