I actually donated thru a Facebook game. There are several options listed on the Times site here:
http://newsfeed.time.com/2011/03/11/five-ways-you-can-help-earthquake-and-tsunami-victims-in-japan/EDIT: I believe PACOM is coordinating military relief efforts in Japan. Maybe their public affairs office can give you a better idea of how to help or perhaps a little feed back might bring more awareness of the plight of smaller Japanese villages along the coast?
PACOM Public Affairs Office (808) 477-1341