G4TV from May 2nd until May 12th is running an auction among other ways to help Japan. If you go over to G4TV.com/Japan you can bid on a myriad of things, even a chance to have former Playboy Bunny Sara Underwood do The Feed from your home.
World Of Warcraft is also offering a way to help with their Cenarion Hatchling.
You can also help by donating to the Red Cross.
This is just a few of the many ways you can help. Even such groups as FansProject have offered donation help, as well as Sony on the PSN is offering donation based themes and avatars.
Celebraties have stood united in saying help Japan. Whether it's Kevin Smith and Jason Mewes, Selena Gomez, or even Uwe Boll, they've all been pushing various donation methods through their outlets(the ones named were to express the spectrum, the complete list is far much longer, too long to type here). IDW, the comic company, has also said they are planning to pursue donating proceeds from their Godzilla comic book or TPBs, to do the same.
Keep in mind I have not listed all the ways you can donate to help. So feel free to add to the list in the comments if you know of more.