While there is no exhaustive directory of nonprofit organizations, there are several directory sites that provide a useful way to find non profit organizations.

The Directory of America’s Charities is a report on charitable organizations which is compiled by US News and World Report. This is a highly recommended resource for finding information about charitable organizations.

Better Business Bureau Wise Giving Alliance - Includes an Accredited Charity Directory

Guidestar provides a database of nonprofit organizations in the US.

Great Nonprofits - a place to find, review, and talk about great—and perhaps not so great—nonprofits.

Also see Nonprofit Resource Centers and Associations by State