Here are some quick facts to know about documentation for an IRS tax exempt nonprofit organization:
Make your annual returns available to the public. While you don't need to go out of your way to meet someone's request, you should make these documents (your 990 forms and your application for exemption) reasonably available to the public. Be ready to provide them if someone requests them. If someone requests them in person, you should make the documents available immediately. If the request is in writing, you have 30 days to provide a copy of the information, unless it makes the information widely available.
Donor lists can be private. Generally, you aren't required to provide anyone with your donor list, even if its in your Form 990, unless you're a private foundation or a political organization.
Keep a copy of your exemption letter on file. This is important for soliciting grants, for any state or local tax issues and for showing potential donors.
Draft and keep a good conflict of interest policy. You might have already done so, when you filed for your tax exemption paperwork. If you haven't already prepared a conflict of interest policy, then you should draft one. One thing such a policy typically does is tell the Board of Directors what they need to do in the event that there is a conflict of interest with a board member, in light of a particular decision. For example, a board member may own a printing shop and the tax exempt nonprofit might have a large printing job to do -- so should it hire the board member's printing shop for the job? At a time like this, there need to be specific measures in place to prevent any conflict of interest on the board.
Compensation policy should be concise. If your tax exempt nonprofit organization decides to pay officers (or board members), it's good practice to have a policy in place for that. Generally, it's good practice for the tax exempt nonprofit organization to collect information on comparable salaries for that position, in order to establish that the amount paid is reasonable. There should also be procedures on how to adopt any decision relating to compensation, in order to avoid potential conflicts of interest.
Do due diligence on recipients. If your 501(c)(3) tax exempt nonprofit organization gives money to other nonprofit groups or organizations, it's good practice to do due diligence on the recipient organizations. Although private foundations are generally subject to expenditure responsibility rules, it's still good practice for a 501(c)(3) pubic charity to keep tabs on the organizations they give to, in order to make sure the money is being put to a use that fits within the 503(c)(3)'s exempt purpose.