Personally, I always donate to the Tzu-Chi Foundation because I know they put nearly 100% of their funds to work on the ground, using volunteers who organize rescue efforts right there on the streets where it’s needed most. We’ve donated to this group many times over the years, following natural disasters, and we’ll do it again on this one, too:
http://www.us.tzuchi.org/usa/home.nsf/other/donateCharity

 

Here’s where you can see other resources for giving aid to those impacted by this disaster in Japan:
Emergency aid to Japan