http://www-sul.stanford.edu/depts/gis/web.html - very well-organized site with some special topic areas as well as the main clearinghouses. Check out the site's web bookmark file for even more sites.
https://wikis.uit.tufts.edu/confluence/x/k4BL- Tufts GIS staff maintain a listing of GIS data sites concentrating on international and US national clearinghouses, as well as New England states, cities and towns.
Harvard Geospatial Library - online geodata repository with map and keyword search through FGDC metadata.
GIS Data Sources - An extensive list of GIS data sources maintained and updated by the Harvard College Library.
More GIS Data Sources - An extensive list of GIS data sources maintained and updated by the Center for Geographic Analysis.
http://libinfo.uark.edu/gis/datalinks.asp - well organized data resource guide to state and national data.
For quick easy access to a multitude of nationwide data sets for the US, check the National Atlas (http://nationalatlas.gov/) - for data download, go to the link for "Mapping Professionals" and then "Raw Data". If you are doing a national level GIS project or looking at a large region, this is a great site to use. If you want just parts of the US, use the National Map web site from which you can clip regions - http://nationalmap.gov/.
http://www.collinssoftware.com/freegis_by_region.htm- this is an excellent and extensive list of city, metropolitan, and state data sets, plus some good international data links, from Collins Software out of Houston, Tx.