Guidestar - register for free access and then use the Advanced Search feature to screen by various criteria. Most records provide IRS Form 990s with financials.
Charity Navigator - screen by location, keyword and compare to related organizations
Organization web sites & offices - you can request 990s for most recent 3 years and the original 1023 filing for nonprofit status, if filed after July 14, 1987.
Facts and Figures - many lists from 1998+ of top fund-raisers, corporate giving, foundation giving, online fund-raising, biggest donors, county-by-county generosity, etc. plus articles on studies by other organizations
New Nonprofit Almanac Information Desk 1 HD2769.2 .U6 N47 2002 - 1977-1998 state by state analysis including employment & financial data. Update with the next sources.
Better Business Bureaus - brief reports on local charities and for-profits, mostly indicating whether or not there have been recent complaints, and if resolved.
Charity Navigator - on the largest 3000 501(c)3 charities that solicit individual givers