If you want to donate, this is a good site which makes it easy. I read that the Japanese Red Cross Society was the first to respond.
Other organizations where you can donate. These are reputable US based charities.
Shelterboxusa provides emergency shelter in disasters and are sending their boxes to Japan. An organization based in the UK, their site has international links.
Page with a list of uptodate information, includes live streaming from major media and twitter with real time updates
Excellent post by a garden blogger in Japan with even more information, personal story and more places where you can help