Well, after I posted that Charity Watch link, I was looking at their site in more depth and am not sure it's the one I was remembering! I found another page with links to SEVERAL such sites that help evaluate charities here:
Effective Donating To Help You Give Wisely
http://www.heartsandminds.org/links/givelinks.htm
A few years back the Goodwill organization is the San Jose area was rocked when the director of one store had sold the good donations to furniture stores and pocketed the money. It worked so well, she got three of her sisters involved and they ran separate stores in the area. The lavish lifestyle finally got someone to look into the matter and the result was they were said to be clearing over $20,000 per month per store. I read the story right here on Freerepublic so maybe its available somewhere.