Going to just post the link here and say that it gives a list of organizations one can donate to besides the obvious ones.
Blog For Japan
There are more that are helping, many without announcing that they are doing so. Individuals and groups inside Japan doing whatever they can. People are still in towns without any help. Over time they will need so much since so much has been lost.
If you want to donate to help out animals affected by this disaster, the above is the donation page for groups for Animal Rescue in Japan.