I just found a very interesting exercise of transparency in peer review on a top scientific topic (climate change) in a top scientific journal (PNAS) by a top researcher (Prof Lindzen, MIT). Note that Prof Lindzen portrays a minority scientific view, he thinks climate change forecasts are uncertain and might be overestimating warming:
"Lindzen-Choi ‘Special Treatment’: Is Peer Review Biased Against Nonalarmist Climate Science?" by Chip Knappenberger. June 9, 2011.
I found this after reading the NYT article "Clouds’ Effect on Climate Change Is Last Bastion for Dissenters" by J Gillis, April 30, 2012.
Disclaimer: I post this becuase it is a very interesting and unique case of how peer review works inside a top journal (for good and for bad). This does not mean I support Prof Lindzen's scientific work (my expertise is in fire dynamics).