• African Union - The former Organization of African Unity is comprised of 54 of the continent's states, and has a vast slate of interests and objectives: solidarity, defense, peace, human rights, development, education, poverty, inter-state economic integration, etc.
• Arab League - Use “Select Language”. A 22-member group of states concerned with the region's economic improvement, dispute resolution, and coordination of political interests

• Asia-Pacific Economic Cooperation - 21 Pacific-rim countries aiming at economic cooperation, free/freer trade, and sustainable growth
• Commonwealth - Commonwealth of Nations is a 53-member association of former British-empire territories. Objectives and interests include peace, democracy, individual liberty, free trade, equality, and development  
• East African Community - Regional economic cooperation, with a stated goal of a political federation of states
• European Union - Political-economic union of 28 member states
• International Criminal Court - The ICC is an IGO and international tribunal that tries cases of war crimes, genocide, and crimes against humanity
• International Criminal Police Organization / Interpol - International organization of police forces. Political Handbook of the World identifies Interpol as an IGO, but Wikipedia calls it an NGO. If you define an IGO as a group of nations, then Interpol is arguably an NGO. Or it might have qualities of both
• Inter-American Development Bank - IDB is the largest source of development financing in Latin America and the Caribbean
• Islamic Development Bank - Finances infrastructure, modernisation, and education projects in its member states and non-member Muslim countries
• OPEC (Organization of the Petroleum Exporting Countries) - A cartel of oil-states with the fairly limited aim of coordinating and unifying the oil production policies of its members
• South African Development Community - 15 states in Africa that want improved social & economic cooperation, political integration, and enhanced security
• United Nations - The largest IGO, it deals with issues of peace, security, development, & human rights
• World Trade Organization - The successor organization to GATT regulates and supervises the international trade of its members 

Other resources on IGOs:   

• Google Custom Search effectively limits your search to IGO links
• IGO library guide at Northwestern University has an extensive alphabetical list of IGOs, including tabs for the agencies of the UN and European Union
• United Nations Digital Library - Documents, speeches, votes, public domain publilcations, etc.
• Harvard Law School - Page defining and describing IGOs.

Technically, at least, NGOs do not promote a government agenda. However, many NGOs are funded by government – for example, a lot of non-military government foreign aid is channelled through NGOs. The Greenwood Encyclopedia of International Relations diplomatically calls this situation “not entirely unproblematic” (1172), which might be one reason some NGOs (like Human Rights Watch) shun government funding.

•  Acumen Fund - An American “transformative” investment and loan organization supporting projects to reduce global poverty
• Amnesty International - AI’s objective: "to conduct research and generate action to prevent and end grave abuses of human rights, and to demand justice for those whose rights have been violated."
• Association for the Prevention of Torture (APT)  - International organization focussed on prevention of torture, or cruel and degrading treatment
• Barefoot College - Development activities in Least Developed Countries
• BRAC (Bangladesh Rural Advancement Committee) - Largest development NGO in the world, working to reduce poverty, illiteracy, and disease
• CARE (Cooperative for Assistance and Relief Everywhere) - International humanitarian and development agency
   

• Cultural Survival - A small American NGO dedicated to the defense of the human rights of indigenous peoples
• Food for the Hungry (FH) - International Christian relief and development organization
• Greenpeace (Canada) - Peace & environment NGO concerned with issues like deforestation, overfishing, genetic engineering, & nuclear power
• Human Rights Watch - Conduct research, raise awareness, advocate for basic human rights (e.g. freedom of religion; freedom of the press), and oppose violations of rights (e.g. capital punishment; discrimination based on sexual orientation)
• Médecins Sans Frontières (Doctors Without Borders) - “Doctors” was in the vanguard of the “without borders” NGOs, and has a reputation for providing medical assistance under conditions of great duress and difficulty. The vast majority of its funding is from private philanthropists, meaning the organization is independent of the institutional interests of governments
• Oxfam - Supports development programs, disaster response and anti-poverty initiatives
• Save the Children - Provides relief and support for children in developing countries
• World Vision - Christian humanitarian aid, development, and advocacy

• WANGO (World Association of Non-Governmental Organizations) - An umbrella organization that facilitates partnership, communication, and resource-sharing among NGOs. Their directory of members (there are many thousands of them) is here.