The Bellona Foundation
Based in Norway, the Bellona Foundation is an environmental group that specializes in nuclear safety, particularly relating to the operations of the Russian Northern Fleet in the Kola Peninsula. Available at this site are some extremely detailed reports on the subject, including a fascinating look at the Northern Fleet's primary submarine base.

Center for Contemporary Conflict
The research institution of the National Security Studies Department of the Naval Postgraduate School at Monterey, California.  Releases a number of regular analytical products online, including its Strategic Insights series.  

Center for Nonproliferation Studies
...at the Monterey Institute of International Studies.

Center for the Study of Intelligence
CIA's academic center, which publishes the in-house Studies in Intelligence, handles the Cold War declassification project, and conducts research into the business of intelligence. For those interested in a serious treatment of the art and science of intelligence production and analysis, this is an important site to visit.

Centre for Defence and International Security Studies
...at Lancaster University, U.K. Home of the CDISS "Missile Threats and Responses" resource base, your one-stop source for information on ballistic and cruise missile threats.

Chiefs of State and Cabinet Members of Foreign Governments
CIA's current guide to world leaders.

Conflict Studies Research Centre
The CSRC is part of the British Army's Doctrine and Development Directorate, and seems to be roughly analogous to the U.S. Foreign Military Studies Office.  It routinely publishes a number of excellent analytical products, mostly focusing on the former Soviet Union and European regional security.  Among these is Dr. Mark Smith's Russian Chronology series, documenting recent developments in Russian domestic and foreign policy. 

DFax Home Page
Home page of DFax, a project devoted to the use of information technology in promoting understanding of defense and international security research. Includes the extremely valuable online editions of Military and Arms Transfer News, International Peacekeeping News, Nuclear Proliferation News, and the reports from the UN Consortium on Disarmament.

FAS Intelligence Resource Program
Operated by The Federation of American Scientists' John Pike, this site is probably the best privately-run resource on technical intelligence issues available on the web. Includes an imagery library that contains declassified samples of product from strategic systems such as KH-12, all the way down to tactical systems such as TARPS. This is a must-see.

Foreign Military Studies Office
Fort Leavenworth's FMSO has its roots in the Soviet Army Studies Office, which conducted open-source research and analysis of Soviet/Pact doctrine, organization, and capabilities. Today, it is the U.S. Army's general foreign military assessment center, providing much valuable literature on everything from information warfare to the Russian experience in Chechnya. It also hosts Red Thrust Star (the recently discontinued print journal of the OPFOR at Fort Irwin), and Special Warfare (in-house of the JFK Special Warfare School).

Institute of International Studies
...at the University of California at Berkeley.

Intelligence and Counterintelligence Home Page
Very complete collection of links pertaining to intelligence and national security issues, including terrorism, weapons proliferation news digests, and a number of official sites.

International Relations and Security Network
The Center for Security Studies and Conflict Research at the Swiss Federal Institute of Technology, Zurich.  Quite a comprehensive site, with a huge number of research links and a Russian Security Project.

The Jamestown Foundation
Jamestown is a unique organization founded in the early eighties to assist asylees and defectors from the Soviet Union and Eastern Bloc countries. Today, it continues to monitor developments in the former Soviet Union (FSU) and seeks to foster democracy and free enterprise therein. Its Monitor provides some of the best regular commentary and analysis on FSU issues available online; I have found their treatment of military issues to be especially useful.

Military Review
Official journal of the Command and General Staff College, Fort Leavenworth, Kansas.

Naval War College Review
Official journal of the U.S. Naval War College, Newport, Rhode Island.

Parameters
The "senior professional journal of the U.S. Army," published by the U.S. Army War College, Carlisle Barracks, Pennsylvania.

Post-Soviet Armies Newsletter
Elisabeth Sieca-Kozlowski maintains an excellent site devoted to the graduate study of military and security institutions in the former Soviet Union, with a focus on non-tactical subjects such as military sociology and civil-military relations.