Early on I heard from several people asking why I didn't have donation information here. I have been hesitant to link to particular charities (even though I have linked to particular news sites) because I didn't feel qualified to choose. The Japanese people I have emailed with since the earthquake are honestly more concerned with knowing that they are not alone in this disaster. They appreciate all the tweets and blog comments giving them support.
But there is no doubt that recovery is going to be a huge, long-term, and expensive effort. Money will be needed, and if you can help by donating then please do. So many people are holding fundraisers and others have set up online donation websites. But do be careful. We are already hearing about donation scams.
Please consider spending some time reading the information on the Charity Navigator site. It gives warnings on how to watch out for scams and telemarketers.
Some organizations like the Red Cross have made it very easy to donate, by texting, using Paypal, iTunes, Amazon, etc. Some have set up specific accounts for Japan relief, while eithers are drawing from their general funds and will need money to prepare for the next disaster.
I have added a couple that you might not have thought about recommended by friends I trust, but you should go with your own heart.