Community Foundations[1] such as the Silicon Valley Community Foundation can receive stock donations that are tax-deductible to the owner. If the donation was in dollars it would also be deductible for the owner, but the owner would need to sell the stock first, which would mean paying capital gains taxes.
Additionally, if the entities receiving the shares happen to be C corporations (which I believe can have 501(c)(3) status), they can deduct the lesser of: (i) 70% of dividends received on the stock; or (ii) 70% of the corporation's taxable income. As such, the implied tax rate on any dividends received from the shares would only be 11.88% (30% * 39.6%), assuming the corporation is in the 35% ordinary income bracket. This is important for 501(c)(3)'s, too, because there are plenty of exceptions to the general notion of "tax exemption" associated with that code section (See, e.g., 26 USC §§ 507-09, 511-15, and 527).
EDIT: of course, this only applies if the company issues a dividend
1. Differences between Community Foundations / donor-advised funds and Private Foundations can be found here: http://www.programforgiving.org/charitable/pages/considering...