Japanese Red Cross Society (English site)
Medicines Sans Frontieres (Doctors Without Borders)
(has a medical team on the ground, but donations go into the general fund)
UNICEF (United States Fund)
Some have commented that Japan is wealthy and needs less assistance than poorer countries. This is a misconception. The nation of Japan has not asked (nor does it expect) financial assistance. However, the organizations listed above are currently expending their resources on helping victims in Japan. Unless these funds are replenished, less funding will be available for their global operations. In disasters on such a monstrous scale, we are all connected.