Websites:

Amnesty International
Full text of human rights reports from countries in the region.

Cairo Institute for Human Rights Studies
Website of the CIHRS, an independent regional non-governmental organization promoting human rights and democracy in the Arab Region. Provides access to publications, press releases, articles and more, in English and Arabic.

Freedom House: Middle East and North Africa
News and reports from the UK based human rights organization.  Country reports from annual publications like Freedom in the World and Countries at the Crossroads are available here.

Human Rights Watch: Middle East/North Africa
Links to publications from Human Rights Watch.

Middle East Human Rights Links
A long list of online resources from the University of Minnesota's Human Rights Library.

Office of the High Commissioner for Human Rights
This UN agency reports on issues in the region.

United Nations High Commissioner for Refugees: Middle East
Website of the UN's refugee agency, containing feature stories and information about the UN's work for refugees around the world as well as databases of news, publications, and links. Searchable by country.