With the death toll now numbering more than a 1400 and climbing...
For us outside of Japan we can offer no physical help, so contributing to disaster aid/relief organizations is the next best option. Here’s a useful list compiled by Time Out Tokyo :
The Cause Action website has an extensive list of groups accepting donations for disaster relief efforts, ranging from Yahoo! to the Democratic Party of Japan. Some are payable by bank transfer, in case you don't have a credit card, though most of the information is currently only available in Japanese. See the complete list here.
The following international sites are recommended:American Red Cross Canpan Fields (Japanese NPO)
Save the Children Non-Believers Giving Aid (scroll down the page for Japan earthquake relief)
NGO Jen (in English and Japanese)
International Medical Corps Association of Medical Doctors in Asia
Hope the worst is over, and Japan can recover soon.