The US Department of Health and Human Services recently announced a new open data initiative, the Community Health Data Initiative, intended to provide tools and data sets for community-level health analysis. As the first part of this initiative, HHS and related government and non-government entities will be collecting and linking to existing data and resources, some of which we've already examined (such as the CountyHealthRankings.org mapplication). The USDA contributes its county-level food and nutrition atlas, useful for visualizing statistics about food deserts, food access, and food insecurity issues, as well as physical activity statistics.
A new website called County Health Rankings analyzes public health statistics for each county in the US, creating state-by-state reports of the healthiest counties. The website, a joint project of the Robert Wood Johnson Foundation and the University of Wisconsin Population Health Institute, analyzes healh factors (statistics about disease incidence, tobacco use, etc.) and health outcomes (such as life expectancy) to create county-by-county rankings of each state. These rankings are then mapped for each state, using Flash-based Fusion Maps software (not free/open source) so that users can drill down to access county-level data.
The Illinois Department of Public Health has an excellent dataset generator for every Illinois county and MSA across the state. In addition to disease and mortality statistics, you can integrate a wide variety of related demographic and socioeconomic data.