Required reading:
http://reprap.org/wiki/Calibration
http://reprap.org/wiki/Triffid_Hunter's_Calibration_Guide
http://richrap.blogspot.ca/2012/01/slic3r-is-nicer-part-1-settings-and.html
http://richrap.blogspot.ca/2012/01/slic3r-is-nicer-part-2-filament-and.html
Suggested reading:
http://reprap.org/wiki/DeveloperBookshelf