If you're a small, tax-excempt organization whose gross receipts are $25,000 or less, you may now be required to file electronically.

From the IRS Web site, via Nonprofit Law Blog:

Beginning in 2008, small tax-exempt organizations that previously were not required to file returns may be required to file an annual electronic notice, Form 990-N, Electronic Notice (e-Postcard) for Tax-Exempt Organizations not Required To File Form 990 or 990-EZ. This filing requirement applies to tax periods beginning after December 31, 2006.

Read more about the e-Postcard.
e-Postcard FAQ