For anyone who doubts that the IRS means business when it requires tax-exempt nonprofit organizations to file an annual Form 990 (in e-postcard form, for the smaller organizations), its June 8th announcement should serve as a wakeup call. The IRS revoked tax-exempt status for a whopping 275,000 organizations, all of which had failed to file the required paperwork for the last three years.
The IRS even published a list of the organizations' names, at www.irs.gov/charities/article/0,,id=240099,00.html.
Some of the groups on this list may simply have been defunct. But it's likely that others didn't understand that the requirements applied to them, due to changes in the reporting requirements over the last few years. For a full summary of these reporting requirements, see Nolo's article Many Nonprofits Must File IRS Form 990-N to Stay Tax-Exempt.
And for help complying with these and other requirements to keep your nonprofits tax exempt status, see Every Nonprofit's Tax Guide, by Stephen Fishman (Nolo).