Al Bab Great site for all things Arabic.  As the name implies, really a gateway to just about any research one wishes to do.

CIA World Factbook The CIA’s open source document covering every country on earth.

National Archives on Terrorism  Repository of U.S. policy documents related to terrorism, along with just about every link in existence on 9-11.

al Jazeera  English translation of the most prominent news outlet in the Arabic world.

The Long War Journal Another great reference link to current events.  Also has a healthy archive for research of specific subjects related to asymmetric threats.

The Daily Star  The English newspaper of Lebanon.  Great opinion pieces, as well as being chock full of Middle East current events that the U.S. media fails to cover.

The Jamestown Foundation’s Global Terrorism Analysis Well thought out analysis without political slants.  Focuses on under-reported aspects of terrorism utilizing indigenous prime sources.

RAND Webpage for the RAND think-tank.  RAND does a great deal of theoretical work on insurgency and terrorism.  Type al Qaeda in the search engine to see what I mean.  Also a ton of information on defense issues, most of it free for the taking.

The Defense Technical Information Center Repository of theses and white papers made on the government dime, all downloadable for free.  There’s a company online that sells these papers, basically stealing the work of other people and selling without the author getting a dime.  They sell my master’s thesis.  Go here and get it for free instead.

Jihadology.  A clearinghouse for Jihadi primary source material, original analysis, and translation services.  It’s a little heavy academically, but a great reference for everything from the Arab Spring to foreign fighter influence in Syria.  Doing a college paper on anything related to Jihad?  Check this site out.