"Good Enough Solutions" and the genetics of diseases - this paper from Jake Lusis's group is a great introduction to why co-expression network analyses are important and what they can contribute to the study of complex genetic traits
A General Framework for Weighted Gene Co-Expression Network Analysis - This is one of the initial papers from Steve Horvath and Bin Zhang that describes the WGCNA method including a more detailed look at the statistical aspects.
WGCNA: an R package for weighted correlation network analysis - This is the original manuscript by Steve Horvath and Peter Langfelder that introduces the wgcna package for R.
Steve Horvath's and Peter Langfelder's tutorials for WGCNA R package
Is my network preserved and reproducible? - this paper from Peter Langfelder, Rui Luo, Michael C. Oldham, and Steve Horvath includes details about calculating preservation of WGCNA co-expression modules