You may find this interesting from the FTDNA FAQ:
Many populations used by the Population Finder tool are from the work of the Human Genetic Diversity Project at the University of Stanford. Other population data from published academic work has been added. Below is a list of source papers that document the populations used.
Behar, D. M. et al (2010, June). The genome-wide structure of the jewish people. Nature 466 (7303), 238-242.
Cann, H. M. et al (2002, April). A human genome diversity cell line panel. Science (New York, N.Y.) 296 (5566), 261-262.
Rosenberg, N. A. et al (2002, December). Genetic structure of human populations. Science 298 (5602), 2381-2385.
Rosenberg, N. A. et al (2005, December). Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet 1 (6), e70+
Teo, Y.-Y. et al (2009, November). Singapore genome variation project: A haplotype map of three southeast asian populations. Genome Research 19 (11), 2154-2162.
It goes on to say that customer results are not used, although FTDNA recently did a customer survey which may be used in updating its Population Finder data base.
I have read on these boards that Ancestry used the data base from the Sorensen Molecular Genealogy Foundation but don't know that for sure.