All the downloaded/CD programs handle QCD ... just complete the follow up screens after you enter the 1099-R to indicate the QCD amount. 

All versions of TurboTax handle QCDs.

When you enter the From 1099-R reporting the distribution, TurboTax will ask you if any of the distribution was transferred to charity, and, if so, how much was transferred to charity.  TurboTax will exclude the QCD amount from the amount that is taxable and will include "QCD" on Form 1040 line 15b or Form 1040A line 11b to indicate that the amount excluded was the result of a QCD.