I also mentioned that Christian B had created quite a nice spectroscopy guide to support his new software called "SpecInti". This guide gives his personal advice on how to acquire and process spectra, and while it is specifically oriented on how to use his new software, it provides a lot of great advice on his whole approach, including exposure times, darks acquisition, flats, normalizing, instrumental response correction, de-watering, etc.
http://www.astrosurf.com/solex/specinti1_en.html