The Charity Commission is the regulator for charities in England and Wales. Their Register of Charities holds details of organisations that have been recognised as charitable under law.
Charity Navigator is the U.S's largest evaluator of charities. Their ratings are based on examination of a charity's financial documents as well as the charity's accountability and transparency.
GiveWell evaluates non-profits and then publishes the full details of their analysis in order to help donors determine where to give.
ANCNC is Australia's independent national regulator of charities. They provide a searchable database of charities, as well as provide fact sheets and guides useful for Australian charities and not-for-profit organizations.
The Better Business Bureau provides information and evaluations about U.S. charities in order to assist donors in making sound giving decisions and to foster public confidence in charitable organizations. They have a searchable database of U.S. charities, as well as a process to allow individuals to file complaints.
The FTC provides a list of tips and advice for evaluating charities and avoiding charity scams. The information is useful for evaluating all organizationa, not just U.S. based charities.