Ezra Klein thinks that political organizations are worthwhile charities.
If you donate money to a food bank, it can provide only as much food as your money can buy. If you donate it to a nonprofit that specializes in food policy issues, it can persuade legislators to pass a new program - or reform an existing one - that can do much more than any single food bank.
So he winds up giving his money to support a think tank whose employees are somewhere around the 95th percentile of the income distribution, in the hope that they will help tilt the rent-seeking in Washington in a direction that he likes.
If you need help finding a charity, you can look at something like Givewell. Theirs is not the only model I can think of for sifting through charities. It is possible that a "recommendation engine" along the lines of movie recommendation engines would work just as well or better. It depends on what you think of the wisdom of crowds, I suppose.
An example of a charity to which I contribute is the Seed Foundation, which supports a charter school for at-risk children in the Washington, DC area. It turns out that the school was mentioned favorably in Waiting for Superman, which I have yet to see. I visited the school many years ago, and I was impressed with the level of effort on the part of the students and teachers.
I think it is actually sort of sad for a policy wonk to settle on the idea of making donations to an organization of policy wonks. To me, it suggests a very narrow comfort zone.