I remember reading a short article in Ms. Magazine (or maybe a short piece of text off-set on one page) about an organization that donated money to a particular elementary/secondary school for girls in Africa (unfortunately, I don't remember the country). All the money raised went directly to pay for the tuition of the students. The more money they raised, the more scholarships they could give out. I also don't remember what year I read this - it could have been as far back as 1999. The magazine gave the contact information for this organization (or possibly it was the school itself?) in the hopes that people would contribute money. I seem to remember something like $50 would pay for an entire year of schooling for one girl.
In the magazine "Off Our Backs: A Women's Newsjournal" i found an article from Nov/Dec 2003.Vol.33, Iss. 11/12; pg. 19, by Lisa Kays who is described as: "Lisa Kays was a Peace Corps Volunteer from 1998-2001 in Benin, in West Africa and worked at the time this article was written for a program that grants girls' scholarships to African girls. She has researched, written on and given trainings on gender and international women's issues for publications and for non-profit organizations. She maintains her ties to Benin and spent time there this summer on a professional visit." If the article you were searching for was from as far back as 1999, Ms Kays was in Benin at the time.
Looking for Lisa Kay on the internet, i found contact information for her: lkays@interaction.org if you want to communicate with someone who has done work out there.
The issue of donating to an organization is an issue of development. "Development" as a concept has come to mean a number of different things to different people and groups based on what they think constitutes the real growth of a people and the use of their resources. The development that the World Bank attempts to impose on underdeveloped countries is different than the development proposed by the theorist Amartya Sen, for example. There are a number of ways that traditional 'development' practices are being rethought, many of them on the ground in underdeveloped countries, and perhaps as well in International Development Studies courses in universities around the world.
The Interaction page that Lisa Kays is associated with is definitely related to African development issues:
http://www.interaction.org/alpi/
According to the website of interaction.org, they are "[t]he largest alliance of U.S.-based international development and humanitarian nongovernmental organizations," and this site should be of use in finding organizations you can donate to in the future.
The website idealist.org may also be of use in this regard. Their slogan is Action Without Borders. Using their search function with the terms 'development' and a region you are concerned with will yield information on organizations, some of them that the website will have checked out and see their work as ethical.