1. Online Data Catalog Sites
Stanford Libraries and Academic Information Services
http://www-sul.stanford.edu/depts/gis/web.html - This is a 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 site.
Tufts GIS Data Resources Guide
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 University - Cartography and GIS Links
http://hcl.harvard.edu/research/guides/cartography/resources/online.html - This site has useful links to both GIS and map sites.
University of Arkansas Libraries - Geospatial and Attribute Data Links
http://libinfo.uark.edu/gis/datalinks.asp - well organized data resource guide to state and national data.
US National Data Sets
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/
Free GIS Data by Region - Collins Software
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.