American Political Science Association's web site
Atlapedia Online contains information and maps for each country in the world
Central Intelligence Agency
Conflict Processes Working Papers contains papers from the Conflict Processes section of the American Political Science Association
Electronic Embassy contains links to information to all the embassies in Washington, DC
EmbassyWeb.com  provides a listing of diplomatic offices and addresses worldwide.  It also contains a listing of other international affairs links.
European Union
Flags of All Countries from Information Technology Associates.  Also offers basic information on the countries
Foreign Affairs Magazine also contains links to other international affairs sites on the web.
Glossary of World Cultures
INCORE is the Initiative on Conflict Resolution and Ethnicity, an online research digest devoted to sharing information on ethnic conflict.
Online Intelligence Project contains world reference materials divided by region.
Online Journal of Peace and Conflict Resolution
Peace and Conflict Studies published by the Network of Peace and Conflict Studies.
Project Vote Smart
Public Diplomacy Calendar provided by the US Information Agency
Specific Country Information contains international news and reference materials.  It  focuses primarily on Africa and development issues but contains links to other regions of the world and political science links.
United Nations
U.S. Army Country Studies and Area Handbooks
United States Institute of Peace
US Department of State
World Chiefs of State and Cabinet Members list from the CIA
World Population counter shows current world population and lets you access world population information back to 1970.
 
 

Reference

It is impossible for me to list all the relevant political science and international affairs sites so I've provided other sites with huge indexing of even more sites.

Academic Council on the United Nations System (ACUNS) International Affairs Resources Virtual LIbrary has over 1100 links.
International Affairs Reference Tools from the Yale University Library. There are tons of useful links here.  Take a look.
International Affairs Resources is a listing of international affairs links (SACIS)
International Political Resources on the Net
International Simulation Resources, from the University of Michigan library, provides source information about countries of the world and international organizations for use in debate and political science courses.
Ronald Mitchell's International Relations Resources, from the University of Oregon, has international law, human rights, general international site links
Howard Romanko's Political Science/IR Links, from the University of Arizona, provides links to political science association, journals, organizations, universities, and data sources.
World Communities contains tons of links separated by country and by topic
Nerd World contains political science links