Zyxware Technologies just released open source software that allows to track epidemics, for example malaria.
Excerpts from their blog entry:
The GIS interface uses Google maps to present the data on a real time
basis on a map of the state. Cases of diseases are represented by
markers on the map and easy visual analysis of the pattern and extent
of spread of diseases is possible. The GIS and reporting interface
processes the cases registered and presents reports that can be used by
the Health Department to monitor the situation on a real time basis and
take precautionary measures if required.
And their online demo.