From my uncle via my mother, this web site has some links to charities which are collecting directly for Japanese earthquake and tsunami relief: http://www.interaction.org/crisis-list/interaction-members-support-japan-earthquake-response. Each has a little blurb about what the organization's services are, from front-line responders to long-term reconstruction, from children's groups to services for the disabled. It's a great list, and money is always the most efficient way to help in a disaster (it gets here fastest and is the most flexible form of response). I am not familiar with all the charities; if you want to do due diligence on anybody in particular I suggest Charity Navigator. Charity Navigator has a page of top-rated Japan charities here, as well as guidance on how to go about donating effectively in a disaster.
In some rare cheerful news - a four-month old baby was found three days after the tsunami and reunited with her parents, who both survived. A young woman from Minamisanriku studying in California found out that her family was OK when TV crews filmed them on their balcony, the only surviving house in the area. And this picture, of a survivor reunited with his dog, made me cry. Maybe it's not the same as finding your baby, but the look on that man's face really moved me. (I know the dog doesn't look so good in the picture, but I had a student double-check the caption. The dog is fine and that is the owner.)