State Charity Offices
Some state charity offices now have searchable databases online.
See Maryland's, for example, at http://www.sos.state.md.us/charity/SearchCharity.htm.
State Incorporation Databases
Medical Expenditure Panel Survey
http://www.meps.ahrq.gov/mepsweb/about_meps/index_researcher.jsp
Includes both household and employer survey data -- 39,000 private-sector organizations. "Researchers in government, the health care industry, think tanks, advocacy groups, and universities use MEPS data for policy-related and behavioral research on the determinants of health care use, spending, and insurance coverage, as well as microsimulation models analyzing alternative health care delivery proposals."
This survey also provides estimates of the number of nonprofit employees.
HCUP Nationwide Inpatient Sample (NIS) - Based on the Nationwide Inpatient Sample (NIS), the AHA survey, and Hospital Compare.
http://hcupnet.ahrq.gov/HCUPnet.jsp?Id=CB00E07747154FFA&Form=MAINSEL&JS=Y&Action=%3E%3ENext%3E%3E&_MAINSEL=Hospitals%20Like%20Mine
Education
http://nces.ed.gov/ccd/data_resources.asp - National Center for Education Statistics Common Core of Data has detailed information on public and charter schools.
Address file
http://nces.ed.gov/ccd/pubschuniv.asp - Universe file has basic demographic info by grade, free and reduced meal numbers (FARM) and other indicators, but no performance info.
http://www.schoolmatters.com - Basic info on proficiency by school. Lists up to 20 schools per screen.