I'm only familiar with the analysis given on "giving what we can" but I also think it's dangerous for everyone to rely on this one analysis. I guess there is room for "meta charity" where people donate their time and expertise to figuring out which charities are the most efficient.
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.
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.
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.