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Geographic Names Information System [GNIS] - This site from the U.S. Geological Survey has a Basic Query that enables you to search the database for all U.S. geographic features, an Advanced Search that uses additional fields for more complex searches. This site also enables you to search for features in Antarctica and to search the database for U.S. geographic features using the relevant Census Codes, Class Codes, GSA Codes, and OPM Codes.
World Atlas - A general geographic site for base maps and information. Note, this site does not GIS enabled.
The U.S. Census Bureau (U.S. Department of Commerce) is the most prolific creator of statistics and maps in the country. You will be able to find resources for mapping Census data and much more.
The U.S. Fish and Wildlife Service (U.S. Department of the Interior) creates a great deal of maps for the National Wildlife Refuge program and for the countless reports they publish on animal life in this country.
Forest Service, (U.S. Department of Agriculture) publishes all those nifty maps you pick up at national forests around the country. They also update their own topographic maps for quadrangles located within national forest boundaries.
Geological Survey, (U.S. Department of the Interior) oversees research and work pertaining to the geology of the country. They publish a myriad of maps including topographic, thematic, geological, climactic, and biological just to name a few.