GiveWell, my favorite charity evaluation site, has published its top-rated charities for the year. Their picks: Against Malaria Foundation and Schistosomiasis Control Initiative (please don't ask me to pronounce that).
They explain their process, so you can see if it makes sense to you.
Interesting that both their choices, like last year's top choice, have less-than-great web design. More proof that a good marketing department does not equal a good charity.