There are various places describing the mechanics of doing a factor analysis (in R or SPSS or whatever) but relatively fewer describing what you actually do, the iterative process of deciding factor size, item analysis, etc.  I found these resources useful:

• http://www.psych-it.com.au/Psychlopedia/article.asp?id=364 – which e.g. discusses item removal.
• http://www.psych-it.com.au/Psychlopedia/article.asp?id=277 – describes ‘Fit indices for structural equation modeling’
• http://pareonline.net/pdf/v10n7.pdf – ‘Best Practices in Exploratory Factor Analysis: Four Recommendations for Getting the Most From Your Analysis’
• http://lavaan.ugent.be/tutorial/cfa.html
• http://www.r-bloggers.com/all-together-now-confirmatory-factor-analysis-in-r/
• http://personality-project.org/r/psych/HowTo/factor.pdf
• http://cran.r-project.org/web/packages/FactoMineR/FactoMineR.pdf
• http://www.statmethods.net/advstats/factor.html
• http://rtutorialseries.blogspot.co.uk/2011/10/r-tutorial-series-exploratory-factor.html
• http://stats.stackexchange.com/questions/32669/vss-criterion-for-the-number-of-factors-in-rs-psych-package
• http://pareonline.net/getvn.asp?v=18&n=8 – ‘Determining the Number of Factors to Retain in EFA’
• http://cran.r-project.org/web/views/Psychometrics.html
• nice post on dropping cross-loading items http://stats.stackexchange.com/questions/58757/what-to-do-with-a-variable-that-loads-equally-on-two-factors-in-a-factor-analysi
• https://en.wikipedia.org/wiki/Factor_analysis#Rotation_methods
• https://en.wikipedia.org/wiki/Confirmatory_factor_analysis#Absolute_fit_indices