Over the past few months I've been searching for all the non-profit organizations that accept Bitcoin accross the world.

With that information I've created the Bitcoin Donation Directory - which lists all the organizations by category. Last I checked there was a few hundreds, maybe 250 on the list.
The list is meant to be crowd-source from now on so you can contribute by submitting an entry.

Link: http://givebtc.org/index.php/bitcoin-donation-directory/

There a few interesting categories such as "open-source projects and projects related to distributed systems, encryption and cryptocurrencies" and "Bitcoin advocacy, education and lobbying, Bitcoin associations, Bitcoin and Alt-coins Charity and Foundations and other Bitcoin related projects", in addition to the regular. charities and non-profits.

I hope you find it useful and use it to help a non-profit integrate Bitcoin.