I've donated through the British Red Cross, but there are other options too.
"The Japanese Red Cross has been working on the ground since the disaster began, mobilising 86 teams, made up of around 600 doctors, nurses and support staff, to provide first aid and healthcare and assess the damage and needs of the communities affected.
More than 300,000 people who were evacuated before the tsunami struck have been housed in temporary centres set up in schools and public buildings where the Red Cross is distributing thousands of blankets.
The Japanese Red Cross has agreed to accept donations from the UK."
http://www.redcross.org.uk/Donate-Now/Make-a-single-donation/Japan-Tsunami-Appeal http://www.thejapanshop.com/ which is part of
http://thejapanesepage.com/ has information on the the earthquake and a link to a Google page with various ways to donate as well as links to the American Red Cross and an organisation that accepts Paypal.
The Arashi On community is doing "Fundraising for Japan-- Arashi-style", they're working in collaboration with several fan subbing communities to raise money and have already raised over $6000. You may have to be a member of the community to download anything, but not sure.
http://community.livejournal.com/arashi_on/ If you can afford to please donate, every little helps.
Thanks.