Three things to keep in mind:
1) The Huffington Post provides a list of legitimate organizations you can donate to, as well as timely updates on the situation in Japan.
2) I know you're all savvy readers, but spread the word to friends and neighbors to beware of scammers. A large crop has emerged out of this crisis. (It's disgusting, I know.)
3) Specific needs are still being assessed so you can wait to see where donations are required most, or donate a bit now and a bit later.