You might like:

http://www.givewell.org/

http://www.greatnonprofits.org/

http://www.charitynavigator.org/

Disclosure: I work for http://www.globalgiving.org which helps grassroots non-profits from around the world that lack name brand recognition fundraise for their projects. Kiva is to microloans as GlobalGiving is to donations.

Thanks, those are great resources. I'm somewhat suspicious of GiveDirectly being a top charity, because even though there are good reasons to believe cash transfers are effective, there doesn't seem to be much evidence that they are the most effective.

The report itself says "We feel that this intervention faces an unusually low burden of proof, though donors' intuitive reactions to it may vary widely."

EDIT: actually the full report deals with the relative effectiveness of cash transfers in some detail.

I've meet the folks at GiveDirectly and think they are doing great work.

That being said, effectiveness of dollars spent is just one measure of a non-profit. It's similar to asking what's the best food. Each person has their own preference, much like each community/country has their own needs. There's no silver bullet to solving the world's problems. It's going to take a wide range of non-profits to address a wide range of problems. When determining your giving, a diversified approach will likely give you the biggest long term impact.