Like anything that can be done easily online, there are of course scams to avoid. Here is a list of reputable organizations that make it easy to donate what you can to help the people of Japan.
Donations are accepted in any amount. They accept Visa, MasterCard, AmEx and Discover.
Charity Navigator offers this advice:
Knowing that people are desperately in need of food and water, it is hard not to want to pack up a box of supplies and send it to Japan. But this type of philanthropy is simply not practical or efficient. Even if mail could get to an impacted region, no one is set up to receive these goods, much less organize and distribute them to the victims. Furthermore, charities are often able to partner with companies to acquire large amounts of in-kind donations such as bottled water and new clothing. Instead of boxing up and sending your old clothing, have a garage sale and turn your used goods into cash and donate that to a worthy charity.