Africa Data Dissemination Service
The Famine Early Warning Systems Network (FEWS NET) keeps a lot of interesting environmental, land use and base GIS data.
Africover
Land cover and agricultural data for East African nations (10 nations) in from the Food and Agricultural Organization (FAO) of the United Nations.
Carpe Data explorer
"The Central African Regional Program for the Environment (CARPE) is a United States Agency for International Development (USAID) initiative aimed at promoting sustainable natural resource management in the Congo Basin." Their website contains a host of links to data. This one seems to be very good!
Quarter Degree Grid Cells for Africa
This site holds shapefiles for the geocoding standard Quarter Degree Grid Cells. The standard was used in the Bird Atlas for the Southern AFrica.
ReliefWeb GIS Data
Shapefile and MapInfo? base layers for Africa.
Safari 2000 Project
Environmental and elevation data for southern Africa. The data were collected between 1999-2001.
SAHIMS GIS DATA
The Southern African Human-development Information Management Network for Coordinated Humanitarian & Development Action(SAHIMS) has collected some GIS data. It covers several African countries and is available for free download.
Lastly I would like to point to an excellent PDF from ESRI which is a collection of articles pointing to successes of GIS from use in area planning, ecology, geology and more: