Are there guidelines in the peer reviewing process on assessing methodology?
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.