For more see the Government Information portal at Columbia. If you are unfamiliar with how the American Government is set up (it's confusing!) please consult this fabulous set of resources from USA.gov.
Department of Homeland Security: On March 1, 2003, the majority of 180,000 employees from 22 agencies were merged to create the 15th department in the federal government. The department has three primary missions: prevent terrorist attacks within the United States, reduce America's vulnerability to terrorism, and minimize the damage from potential attacks and natural disasters.
Department of State: The Department of State is the primary source of foreign affairs information for the U.S. Government and is responsible for implementing the President's foreign policies.
Under Secretary for Arms Control and International Security: The Office of the Under Secretary for Arms Control and International Security Affairs provides policy direction in the areas of non-proliferation, arms control, regional security and defense relations, and export control policy related to materials that might contribute to proliferation or otherwise harm U.S. interests.
Background Notes - U.S. Department of State: Brief profiles of most countries of the world. Includes information on government type and structure, names of major government officials, and an overview of foreign relations.
Don't forget that the State Department has had many versions of their website that can be accessed at their web-archive.
All 15 U.S. Departments Under the Executive Branch
Central Intelligence Agency (CIA): Provides information on foreign intelligence, counterintelligence activities, special activities, and other functions relating to national security.
Annual Worldwide Threat Assessment: A report from the Director of National Intelligence to the House Permanent Select Committee on Intelligence and the Senate Armed Services Committee.
World Bank Development Reports: Reports on economic, social, and environmental state of the world. Published annually since 1978.
Centers, Boards, & Institutes
Defense Nuclear Facilities Safety Board (DNFSB): Congress created the DNFSB in 1988 as an independent oversight organization within the Executive Branch to provide advice and recommendations to the Secretary of Energy regarding public health and safety at DOE's defense nuclear facilities.
George C. Marshall European Center for Security Studies: The Center provides instruction in national security affairs to Europe's senior defense officials; conducts research on European security issues; holds conferences on those issues; conducts specialized regional studies and language training courses.
Institute for Defense Analyses: IDA is a nonprofit corporation whose purpose is to promote national security and the public interest and whose primary mission is to assist the Office of the Secretary of Defense, the Joint Staff, the unified commands and defense agencies in addressing important national security issues, particularly those requiring scientific and technical expertise. To avoid institutional pressures in support of Service positions, IDA does not work directly for the Military Departments.
Institute for National Strategic Studies: INSS was established in July 1984 as an interdisciplinary research institute staffed by senior civilian and military analysts from all four Services. The Institute Director sets the research agenda of the Institute to meet the needs and requirements of the Department of Defense.