The City of Chicago maintains an informative GIS portal with links to base maps, datasets, and specific interactive maps for various applications, such as airport area sound insulation levels, interactive zoning maps, and West Nile virus infection tracking.
The Library of the University of Arkansas has a very impressive collection of international and US geodata repository links - mostly geospatial data and attributes. I'll be poking around in here for hours, I think! A wide variety of topics and well-organized to boot.
A project of Columbia University, "SEDACs mission is to develop and operate applications that support the integration of socioeconomic and earth science data and to serve as an information gateway between the earth sciences and social sciences." In addition to a host of interactive mapplications, they host a large number of academic data sets on a wide variety of topics.
"The North American Religion Atlas (NARA) provides access to resources for the study and teaching of North American religious history within a geographical and multimedia framework. Using mapping technology, users can view data on religion at national, state or county levels. Text, image, and multimedia formats are also available and contribute to greater understanding of the story of North American religion."
"The Electronic Cultural Atlas Initiative is a global consortium of people who share the vision of creating a distributed virtual library of cultural information with a time and place interface. ECAI is a global consortium incorporating scholars in the humanities, social sciences and history; archivists, librarians and curator; members of non-governmental organization; and information technology researchers."
They've got some interesting uses of maps as atlases containing digital storytelling, as well as links to hundreds of maps and geo pieces related to various aspects of culture.
A local New Jersey watershed protection organization sponsors this regional GIS clearinghouse. They've got lots of good content from over the years, most of it focused on the Northeast and environmental data collection/visualization.