Are there guidelines in the peer reviewing process on assessing methodology? Usually an article goes through a peer-review process before it is published, and from what I here it is quite common that the reviewers "demand" some changes.


Are there guidelines for peer- reviewers, especially as the methodological side of things is concerned?
Are  "methodology specialists" incorporated in the process?
This does not really answer your question (because it doesn't deal in detail with methodological issues), but there is a nice journal article that deals with problems of the peer review process in general by evaluating "great scientific works of the past" from the perspective of current social sciences:


Trafimov, D., &amp; Rice, S. (2009). What if social scientists had reviewed great scientific works of the past? Perspectives on Psychological Science, 4, 65-78. doi:10.1111/j.1745-6924.2009.01107.x Available online at http://cda.psych.uiuc.edu/writing_class_material/perspectives_articles/trafimow.pdf


The reference list has some articles on statistical/mathematical methodology questions.



In another interesting article, Gerd Gigerenzer shows how p-values are misinterpreted in current research and null hypothesis testing is made a false requirement for the acceptance of papers by major journals:


Gigerenzer, G., Krauss, S., &amp; Vitouch, O. (2004). The null ritual: What you always wanted to know about significance testing but were afraid to ask. In D. Kaplan (Ed.), The Sage Handbook of Quantitative Methodology for the Social Sciences (pp. 391-408). Thousand Oaks, CA: Sage. Available online at http://www.sozialpsychologie.uni-frankfurt.de/wp-content/uploads/2010/09/GG_Null_20042.pdf




A Google search for "peer review guidelines" brings many hits from publishers and institutions. Maybe some of them deal with methodological issues in more detail.