I agree with Felix Salmon's "Don't Donate Money to Japan" post that everybody jumped on because of the headline. If there's something you can do to help people affected by the tsunami / nuclear meltdown in Japan, please do it! But donating more money probably isn't such an act.
The major bottleneck in well-publicized disaster scenarios usually isn't money. It's the ability to actually get stuff to the people who need it. In Japan, the government is going to be the group on the scene with the most logistical resources, and it's better funded than any relief organization. While relief groups usually have a larger role to play in third world countries whose governments can't do very much, Japan isn't a country of that kind. GiveWell says, "At this time, we believe that the relief and recovery effort does not have what we call "room for more funding," i.e., donations are not likely to improve the effort."
What GiveWell suggests is giving money to Doctors Without Borders (Felix gave $400), since they're excellent at dealing with the next catastrophe, and the one after that. I've given them a fair amount of money myself over the past few years, particularly on the advice of some people who'd been to disaster areas or other places where humanitarian aid was being offered. The consensus is that they do a good job.