GuideStar's database contains data on more than 900,000 public charities, approximately 118,000 private foundations, and nearly half a million other exempt organizations in the United States. Federal 990 forms can be accessed through Guidestar.
Resources compiled by librarians from U-M Kresge Business Library. Categories include links to nonprofit organizations, nonprofit databases, and freely available resources related to financial management, regulations, board governance and fundraising.
The Foundation Center provides this free database where you can find data on grants given per year, including dollar value of those grants, by subject areas. This database also allows you to view data by population groups and recepient location. Additional statistics include aggregate grant fiscal data and top grant givers.
The Nonprofit Almanac 2012
Provides data from 2000 to 2010 on financial and employment trends in the nonprofit sector and attempts to evaluate the role of nonprofits in the U.S. economy.
Blackbaud - Nonprofit Industry Research
Blackbaud is a publically traded company which provides software, services and training to nonprofits.
Library Databases for Nonprofit Statistics
The United States government produces a large amount of data. A list of agencies that compile statistics can be found here