A lot of useful information about the IRS rules for tax exempt organizations can be found in Revenue Rulings.  These are official IRS pronouncements explaining how existing tax law would apply to a specific set of facts.  The IRS has summaries of, and links to, Revenue Rulings that pertain to Exempt Organizations matters on this page of irs.gov, summarized by year.

Unfortunately, some useful Revenue Rulings have been omitted.  I have emailed the IRS about these rulings multiple times, going back to 2007, without result, so I am posting these Revenue Rulings here.

These rulings can be found in other places on the Internet, so they're not really "missing," just missing from the IRS website. There may be other E.O. Rulings not duplicated in the Exempt Organizations archive of published guidance; these are just the ones I have run across in my writing and tax consulting

54-243:
A non-501(c)(3) organization may establish a separate charitable fund. 

63-252:
Five examples of U.S. charities that transmit funds to foreign charitable organizations.  Three do not qualify under 501(c)(3), two do.

64-174:
A foundation that helps local communities establish their own charitable/educational repertory theaters will qualify under 501(c)(3).
 
66-79: 
Contributions to a domestic charity for a specific project of a foreign charitable organization are deductible when the project furthers the domestic charity's own exempt purposes and when the charity exercises oversight of the project.

66-177: 
An organization formed under foreign law which meets the tests for exemption under section 501(a) can qualify as an exempt organization.

70-186:
A nonprofit organization formed to preserve and improve a lake used extensively as a public recreational facility qualifies for exemption under section 501(c)(3) of the Code.

74-587:
A nonprofit organization formed to provide financial assistance to business enterprises in economically depressed areas can be exempt under section 501(c)(3) of the Code.

75-65: 
Contributions by an individual to a domestic charity formed to deal with the problem of plant and wildlife ecology in a foreign country through programs that include grants to foreign organizations and over which it maintains control and responsibility, are deductible as charitable contributions.

81-28: 
A nonprofit organization that provides housing, transportation, and counseling to hospital patients' relatives and friends who travel to the locality to assist and comfort the patients qualifies for exemption under section 501(c)(3) of the Code. 

2004-27:
Tax avoidance schemes; meritless “corporation sole” arguments. This ruling emphasizes to taxpayers, tax scheme promoters and return preparers that, while a “corporation sole” is a legitimate corporate form that may be used by a religious leader to hold property and conduct business for the benefit of the religious entity, a taxpayer cannot avoid income tax by establishing a religious organization for tax avoidance purposes.  

Missing IRS Rulings