I've found Givewell to be incredibly analytical and thoughtful in their analysis of how to get the most bang for the nonprofit buck, and I always consult them before giving. I'd encourage everyone to visit GiveWell next time they have some reason they're going to give money (or some area they want to give to) but they're not sure to whom to give.

For an example of their work, an analysis of the value of giving cash directly to those in need (instead of, say, a cow): http://blog.givewell.org/2012/12/26/the-case-for-cash-2/

Their top recommended charities: http://www.givewell.org/charities/top-charities

(Fwiw: before I entered tech I was a consultant helping big foundations (like Gates, Packard, etc.) assess their performance (as part of http://www.effectivephilanthropy.org). So for a tech person I consider myself reasonably well-versed in nonprofit evaluation--and how difficult it is.)