What an unimaginable tragedy. The Church is still formulating its disaster response through Catholic Relief Services and Caritas Japan. Our bishops should have clear instructions on how we should help very soon.
Charity Navigator, an organization that monitors charitable groups (and unfortunately, bogus groups) understands our desire to do something right now but counsels us:
"Wait and see: While we all feel an urgent need to help immediately following a massive disaster, some donors may want to wait a few days before donating. By then, charities should have a more clear plan of how they’ll provide aid."
Japanese Red Cross is already on the scene. If you feel you must donate right away, Bay Area Red Cross has a webpage where you can send a donation specifically for the Japanese disaster.