After some research, I located two groups who are on-site in Japan, helping animals made homeless by the earthquake/tsunami. If you have additional links/information, please leave them in the Comments section. If you have problems leaving a comment, click Preview before Post.
Here are some links:
Arkbark has a Paypal donation site. You can view the Paypal pages in English - click on the pull-down at the top right to toggle between Japanese and English. But you'll have to convert Japanese yen to your currency on another page. Here's a currency converter link:
If you donate 2,000 yen, it comes out to US$24 and change.
Another group is actually three groups: HEART-Tokushima, Animal Friends Niigata and Japan Cat Network. Here is their blog and donation link:
The Chipin donation widget wasn't working for me yesterday, but the donations have increased since then, so I am assuming heavy traffic is causing the problems with Chipin. (It may go to Paypal, anyway; Chipin can be redirected.)