RPM has a post up about Y and mtDNA lineages, and what they can (or can't) tell us about demographic history. I'm pretty skeptical myself about the broad and detailed deep time inferences some make with these markers (see The Real Eve for an extreme case), but Dienekes points me to a situation where there is some utility to this methodology:
The differential relative contribution of males and females from Africa and Europe to individual African American genomes is relevant to mapping genes utilizing admixture analysis...The European genetic contributions were highest (and African lowest) for the Y chromosome (28.46%), followed by the autosomes (19.99%), then the X chromosome (12.11%), and the mtDNA (8.51%). The relative order of admixture fractions in the genomic compartments validates previous studies that suggested sex-biased gene flow with elevated European male and African female contributions. There is a threefold higher European male contribution compared with European females (Y chromosome vs. mtDNA) to the genomes of African American individuals meaning that admixture-based gene discovery will have the most power for the autosomes and will be more limited for X chromosome analysis.
Similarly, Latin America shows strong signatures of asymmetrical gene flow in relation to the sexes. The key I think is that genetic data is a supplement to what we already know, and refines and confirms our hypotheses, the problem tends to be when genetic data is the sole leg upon which to stand, because as RPM notes assumptions of neutrality might not hold across the time spans and geographical distributions that we wish to survey.