I used to and sometimes still have doubts on how certain charity organizations would channel the funds they collect. A bit of research can often yield intersting results which can help you in your decision whether to donate to a certain organization.
For example, after looking into a certain body which looks into kidney related ailments, I decided to stop my donations to them after finding out the head of the organization flies nothing less than first class while travelling on official business. Their flyers and appeal letters come in such fancy packaging too. I feel that they were misusing or not using the donated funds in an effective manner. I promptly ceased my donations to them.
As many have mentioned, if you're in doubt, it's best to donate items rather than cash. But working with such organizations, I know that your $$ tends to go a much longer way if your cash were used to purchase items in a place like Indoneisia for example.
It's not a easy decision to make but go with what you think it's best. Oftentimes, common sense is all that is need with such decisions. If you're a Christian, pray about it and trust that God will direct your efforts to a worthy cause.