I know some people don't consider kiva to be much of a 'charity' since the recipients have to re-pay the loan, but most donors don't take the money back and instead re-loan to someone else, changing more lives. And then most add even more money to their pool so that they can loan to more people and groups. http://www.dhammaloka.org.au/
and the nuns' monastery building fund
Other bhikkhuni monasteries and funds.
Local temples and Dhamma centers in your area are another option. http://theofferingbowl.com/
Practitioners who need funds to attend retreats or other Dhamma / Dharma activities.