My wife chooses all our charities (mostly animal ones). When it comes time select which to give to, she uses Charity Navigator, which rates charities from zero (worst) to four (best) stars based on financial strength, accountability, and transparency. The methodology uses information from the IRS Form 990 and the charities’ websites. You can read more about it here. In some uncommon cases, donor advisories are issued, which supersede ratings.

I’ve graphed the distribution of ratings for each of the 11 broad categories defined by Charity Navigator, and provided the average rating, which excludes charities with a donor advisory. Interestingly, the distributions are quite similar among 10 of the 11 categories, with the outlier being charities focused on religion; these have notably worse ratings. Among the average ratings, community development charities have a score that is one standard deviation above the mean, while religion is almost three below! Religion charities are also the most likely to have a donor advisory.

Data source: http://www.charitynavigator.org/