Form 990
It is a relief for many organizations to learn that IRS Form 990, the annual "Return of Organization Exempt From Income Tax," is not required when gross receipts are less than $25,000. It might be a better idea to file a "blank" Form 990, than to not file at all:

Most important of all, the normal IRS three year "statute of limitations" is triggered by the filing of a return. If your group does not file a 990 or 990EZ, the three year period never starts, the statute never closes, and there is no limit on how far back the IRS can go in an audit situation.

To file a "blank" return, complete all the identifying information at the top of the return, check the box indicating that gross receipts are normally less than $25,000, sign and date the return, and send it to IRS, Ogden, Utah 84201. Be sure to make a copy for your own records.

Employment Taxes
It is never a good idea to ignore a Form 941, "Employer's Quarterly Federal Tax Return," sent to you by the IRS. If you do not need to file the return, because you had no payroll for the quarter, or because you have no employees, complete the return anyway, and send it in (keeping a copy for your own records.)
It is tempting, when hiring workers for the first time, to treat them as independent contractors rather than employees. Withholding, quarterly deposits, etc. can be such a bother. But misclassification of employees is, by far, the most common issue that IRS auditors raise with non-profit organizations. IRS Publication 539 discusses the factors the IRS considers in classifying workers.
There are times, of course, when workers really are independent contractors. Many organizations overlook the need to report compensation of $600 or more to the IRS. Awards, fees, and similar payments must be reported on Form 1099-MISC, which must be sent to the recipient no later than January 31st, and to the IRS, with a Form 1096 transmittal, no later than February 28.

IRS Audits of Non-Profit Organizations
When the IRS audits a non-profit organization, they normally ask to review the following:

1. Governing Instruments
2. Copy of Exemption letter
3. Minutes of meetings (usually several years worth)
4. Financial records, including check register, canceled checks, bank statements, invoices, receipts, and auditors report and working trial balance.
5. 990's for years before and after year under audit
6. Copies of all other Federal tax and information returns filed, such as 940, 941, W-2, W-3, 1099 and 1096.
7. Pamphlets, brochures, descriptive literature, etc.
8. Newsletters, if the organization publishes one.