There has been lots and lots of talk about "population genomics" in the last few years. For microbes, people have been doing this type of genome wide survey within populations for some time. But for multicellular organisms there have been only a few studies and most of these were limited in scope. Now comes a in depth study of Drosophila simulans published in PLoS Biology. This project, led by colleagues of mine at UC Davis (David Begun is first author, Chuck Langley is senior author) did "light" whole genome sequencing (at the Washington University Genome Sequencing Center) of seven lines of D. simulans and one line of D. yakuba.
There is lots of interesting population genomics, population genetics and evolutionary analysis in this paper. If anyone out there is interested in personal genomics or human population genomics in any way, it is worth checking out this paper as a model for what can be done in multicellular eukaryotes.