Some ways to help:
The Google Crisis Response page for the event lets you donate directly to the Japanese Red Cross.
Several Japanese popular culture writers, including Patrick Macias and August Ragone, are pointing to the Japan Society of New York's relief fund page, where "100% of your generous tax-deductible contributions will go to organization(s) that directly help victims recover".
On that same point, comics and animation writer Mark Evanier links to Operation USA, another organization who uses 100% of the donations for relief efforts.
DriveThruRPG and RPGNow are collecting $5 donations for the Red Cross.