A quick Google search brings up plenty of ways to help the people in Japan that doesn't include "prayers and thoughts," for you atheists out there that want to do more.
The Red Cross is a large, trusted (and of course, secular) organization that sends relief around the world. You can visit their website here or text "REDCROSS" to "90999" to send $10.
Charity Navigator put out their list today. A few listed are faith-based, so do your research.
Facebook also has a page. Again, I recommend visiting websites to ensure that your money is going to actual aid and not to set up prayer groups or hand out holy books.