The Foundation Center has long been a leader in providing resources to the philanthropic community. Their site includes a search form that returns basic information about private foundation funders, as well as links to their 990s. They offer a number of other fee-based services for foundation researchers.
Guidestar is another source where you can search for basic information about nonprofits (i.e. public charities) and private foundations and obtain their 990s.
NOZA provides access to this database of 990-PF tax returns. This project was started several years ago by Grantsmart and contains publically-available data received from the IRS. To search NOZA's companion database containing more than 1,000,000 foundation grant records (also free), please visit www.nozasearch.com.