NonProfit Gateway
This is the big one. A network of links to Federal Government information and services. Fully searchable.
USDA Nonprofit Gateway
Maintained by the United States Department of Agriculture.
Department of Education Nonprofit Gateway
The DoE has organized information from across their web site and presented it here.
HUD Nonprofit Center
Information from the Department of Housing and Urban Development.
The Attorney General of the United States
Includes an extensive Handbook for Charitable and Nonprofit Organizations.
NIST Advanced Technology Program
The National Institute of Standards and Technology sponsors a program that helps nonprofit organizations with research and development initiatives.
The Small Business Administration Nonprofit Home Page
It looks like this site has seen better days, however it does contain information that may be of use.
The Internal Revenue Service
Frequently Asked Questions About Tax-Exempt Organizations.