I would like to suggest two methods papers that are quite thought provoking. These are on applying the phylogenetic species concept and there is considerable discussion of intraspecific phylogeny and examples using mtDNA and other tools. Check your local university library or find them on the net if you can.
Davis and Nixon 1992: Systematic Biology 41(4):421-435 Brower 1999. Systematic Biology 48(1):199-213