Genomic studies often go for the biggest bang, the largest scope. There's the 1000 Genomes Project for people and the 1001 Genomes Project for Arabidopsis thaliana, which is still underway, among many other studies with large sample sizes.
At his blog, Pathogens: Genes and Genomes, Nick Loman has an "uber list" of such large-scale sequencing projects that have been published. Currently topping his list with the greatest number of samples is a University of Washington-led study of 2,007 Caenorhabditis elegans, followed by a study of 1,250 Clostridium difficile samples and the 1000 Genomes Project, which actually includes 1,092 human genomes.
But, Loman notes that there are more studies coming down the pike that could make these projects seem small. He points to the Million Human Genome Project, a 100,000 foodborne pathogen project, and the 100,000 National Health Service patient project as the top contenders to knock the current studies off their pedestal.