CIA
Central Intelligence Agency. A good site for information on countries from around the world right down to GDP and number of political parties.

Counterterrorism Intelligence Capabilities and Performance Prior to 9-11 
House of Representatives Permanent Select Committee on Intelligence, Subcommittee on Terrorism and Homeland Security.

Department of Commerce
As the banner states, the Department of Commerce has a "broad range of responsibilities include expanding U.S. exports, developing innovative technologies, gathering and disseminating statistical data, measuring economic growth, granting patents, promoting minority entrepreneurship, predicting the weather and monitoring stewardship". On-line access to the budget, important calendar of events, and links to individual commerce departments.

Department of Defense

Department of Homeland Security

Department of Justice
Home of the FBI. Links to various D o J organizations, issues and news.

Department of State
Excellent site with access to current policy, press briefings and statements, "Dispatch Magazine", and the organizational structure complete with phone numbers. Too many areas to cover here but well worth a look.

Digital National Security Archive
The Digital National Security Archive contains the most comprehensive collection of primary documents available. The database contains more than 35,000 of the most important, declassified documents that led to US policy decisions.

FBI
"In a world that is changing by the second, the FBI solves ever-increasing challenges more intelligently, and at higher levels."  An excellent, up-to-date site with information on the FBI's national security and criminal investigations.

FedWorld
The Federal Information Network. The National Technical Information Service (NTIS) introduced FedWorld in November 1992 to help with the challenge of accessing U.S. Government Information online. Its mission is to provide a one-stop location for the public to locate, order and have delivered to them, U.S. Government information. Great searchable database.

Federal Emergency Management Agency (FEMA)

Joint Chiefs of Staff

Library of Congress
On-line search of the main collections with links to news, events and other on-line database resources.

NCIX
Office of the National Counter-Intelligence Executive. A great page with access to updates, threats to US business interests as well as news, trends and developments.

NIC
The National Intelligence Council (NIC) is a centre for US government mid-term and long-term strategic thinking and for intelligence community collaboration on substantive issues.

National Geospatial-Intelligence Agency (replaced NIMA)

National Infrastructure Protection Center (NIPC)
The National Infrastructure Protection Center (NIPC) serves as a national critical infrastructure threat assessment, warning, vulnerability, and law enforcement investigation and response entity. The NIPC provides timely warnings of international threats, comprehensive analysis and law enforcement investigation and response.

National Reconnaissance Office
The NRO designs, builds and operates the nation's reconnaissance satellites. NRO products, provided to an expanding list of customers like the Central Intelligence Agency (CIA) and the Department of Defense (DoD), can warn of potential trouble spots around the world, help plan military operations, and monitor the environment.

NSA
The National Security Agency. Links to the mission statement and other useful tidbits of information. Kind of thin but then again that's to be expected.

National Security Archive
Access to the NSA in Washington D.C. Allows an on-line search of the archive's collections and provides links to the Nuclear Non-Proliferation database and others.

Security Policy Board
A new site that provides insight into those factors that set US National Security. A bit slow so be prepared to wait for a bit.

THOMAS
THOMAS is the US Congress on the Internet.  Bills, roll call votes, etc. can be found here.  Searchable.

Today's Global News (Overseas Security Advisory Council, US Department off State)

U.S. Government Documents: The U.S. Intelligence Community (Columbia University Libraries)

U.S. House of Representatives
The header reads "The U.S. House of Representatives' World Wide Web service provides public access to legislative information as well as information about Members, Committees, and Organizations of the House and to other U.S. government information resources". Pretty much sums it up. Need to find out about a specific law or when the next hearing is on a particular issue? This is the place to go.

U.S. Senate
The "other" legislative branch of the United States Government. Includes a full listing of members, committees, etc.

The White House
A great site with a searchable database on speeches, publications, etc. Good links to all manner of White House information and other government information. Includes the Interactive Citizens Handbook which will let you search just about every U.S. government site imaginable.