I have found a few websites that you can donate to if you would like to help out with the situation in Japan. Here is a list of a few organizations that are currently involved with the efforts to assist people who have been affected by the earthquakes and tsunami from this weekend.
Tzu Chi: A Buddhist volunteer organization with 10 million volunteers in 50 countries (about 120,000 in the U.S.) and only a small support staff. All of your donations go to victims without proselytization.
Doctors Without Borders: A humanitarian organization in which doctors provide impartial medical assistance in places stricken by war or natural disasters.
The Red Cross: A famous emergency response organization. It provides neutral humanitarian care to victims of wars and natural disasters.
Global Giving: An organization designed to help people give toward charities they care about to make positive change in the world.
More info can also be found at the Huffington Post.