I prioritize my giving to local, small non-profits. I usually have a relationship with them beyond the check I write (I have volunteered or been a board member).

If you are giving to big charities (because they match up with your values), they have tons of data on what they are doing with the money. They also sometimes have internal funds you can donate to that are earmarked to only be spent on a specific activity -- just ask.

Good advice...I tend to focus on "local" needs, as well...you can often gauge their effectiveness quite easily because you can see efforts and results first-hand...

I've volunteered and served on boards, too...a great opportunity to connect with your "community" and gain a deeper understanding of the issues affecting it...

I've referenced Charity Navigator* a few times, but haven't looked much deeper than that--basically using it as a quick reference.

* http://www.charitynavigator.org/

Checkout GiveWell (http://www.givewell.org/). They are ex-hedge-fund guys who wanted to apply quantitative methods to this very question.

Also, from a personal standpoint, I try to give in accordance with Peter Singer's recommendations that you should help the worst off first (So things like Malaria Nets and de-worming). It's easier to be sure you're making things better if the money goes to treating a life-threatening disease that can be prevented for a few dollars a head.

One thing you can do is contact the organizations and ask for some documents about what they are doing with the money and other data. All organizations waste money or use it ways you might not like. But I think you have to do some research. Ask for the data from the given organization and make an informed decision from there. Any non-profit should have this data available in some form for you.

You can't really control how they use it. But you can see what they accomplished in the past. Look at what they are planning for the next few years. And then evaluate at the end of the year and see if you feel like they did what they said they would.

Do you believe that "non-profits" are making more goodness in the world than for-profits?

Good question...my answer is not always...

But, the non-profits I typically support function as "safety nets", providing niche goods or services that would otherwise be unavailable to their patrons...quite often those are quite basic--food, clothing, healthcare...

You should read Giving 2.0 by Laura Arrillaga-Andreessen. She goes into depth this and many other aspects of philanthropy.