Africa Windmill Project focuses on educating and supporting rural farmers as they work to feed and care for their families. We do this by working directly with the farmers and by supporting other organizations as they work with farmers. Currently Africa Windmill Project is focused in the Central Region of Malawi.
The Africa Windmill Project has a blog where they occasionally post notices about the status of projects; lots of interesting things there. (For those who prefer to review financial data before donating, that can be found by registering with GuideStar.)
I have also in the past had fairly good experiences with International Justice Mission, although you should know beforehand that they are rather assertive mailers:
International Justice Mission is a human rights agency that brings rescue to victims of slavery, sexual exploitation and other forms of violent oppression. IJM lawyers, investigators and aftercare professionals work with local officials to secure immediate victim rescue and aftercare, to prosecute perpetrators and to ensure that public justice systems - police, courts and laws - effectively protect the poor.
International Orthodox Christian Charities, which is, as it says on the tin, an Orthodox organization but is devoted entirely to humanitarian activities, has also been a charity with which I've had good experiences in the past. It has a number of programs.
Any other suggestions?