First off, I strongly suggest not donating to a charity unless they produce a 990 form.
There are still a lot of charities that are flat out scams, like breast cancer "awareness" charities who's board member owns a marketing firm, that creates awareness by calling people and asking for donations to their breast cancer awareness fund. Avoid "awareness" charities. Most of them are complete bunk.
Here are my top three websites for researching charities.
I shoot for a 90% efficiency ratio. But that isn't always possible for all diseases. Sometimes you will have to settle for a 80-85% efficiency ratio. Whenever you find a charity that you like, look it up and see if there are any charities that address the same issue, but perform better.
Also, start looking at the 990 forms for the charities that you do give to. This will help you to evaluate charities that are too small to have 3rd party evaluations.
Also start looking at their Annual Reports to see what they have actually accomplished for the past year. This will be especially important for charities that do not provide services or do research (like political/lobbying charities). Their efficiency ratio will be much lower, but their staff may be doing what you consider to be important work. Avoid charities that are not readily transparent about how their money is spent and what their accomplishments are.
Some exceptions are small charities such as food banks or soup kitchens that do not have any paid staff or management. Those are probably some of the most efficient charities out there.