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.
This is a very useful interface allowing visitors to visualize all U.S. records of cancer deaths over a 50-year period. Epidemiologists and others can drill down to the county level, selecting from dozens of different types of cancer. Data can be output in a variety of formats, including static image for copying and interactive Flash maps.
A good website to read up on it is MapCruzer! and CRAN's site. This tool can use geostatistics and spatial regression as well and read and write geodata. It also has special tools for disease analysis and ecological analysis.
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.