Nikon Corporation made a 100 million yen (over 1.2 million USD) donation to the Japanese Red Cross. I believe donating directly to the Japanese Red Cross is the best way to support the relieve efforts in Japan and to ensure that your money will reach the devastated areas. From the US, the easiest way to make a donation is through Google:
Here is a detailed list of charitable organizations currently involved in the relieve efforts in Japan. You can also see Reuters blog and Charitynavigator on how you can help.
NikonRumors.com will donate a portion of its Google AdSense advertising earnings to help those affected by the earthquake.