Great article in this Monday's Technology Review on different websites/apps set up to help people in Japan, such as Ushahidi, SparkRelief, and Hurricane Party.
I was happy to read about these efforts, and encourage you to participate with them and/or donate on your own.
For monetary donations, InterAction has a list of verified charitable organisations who are accepting donations, which also describes how they will use the funds. Definitely check InterAction or with the Better Business Bureau before donating - there are a lot of scams out there.
For non-monetary donations, you can donate frequent flyer miles, socks, or send hopeful letters. (The sock guy mentioned letter writing as a thoughtful gift the Japanese will appreciate, which I think sounds like a great idea).