I tend towards a variety of non-profit organizations as a rule, but there are certain IGOs of which I am especially fond.
The United Nations (www.un.org) - It has its issues, but the UN revolutionized international relations and the combination of UNICEF, UNDP and UNESCO, among other agencies, have made significant advances in human rights and development issues.
The European Union (europa.eu) - An entire class during my Masters was devoted to this regional IGO. I loved studying the evolution of the organization.
Interpol (www.interpol.int) - Revolutionized the pursuit of criminals across borders.