Japan is one of the richest countries in the world, both in absolute and per capita terms. The earthquake and tsunami have inflicted terrible damage on the country, leading most likely to thousands of deaths and many millions of dollars of property damage. However, as a nation, Japan has ample financial resources to recover from the disaster. Japan was a healthy and prosperous society one week ago, and a year from now the overwhelming majority of Japan's people will still be alive and healthy, and they will still be relatively prosperous in global terms.
By contrast, there are still hundreds of millions of other people around the globe living in conditions of persistent poverty and immiseration. Just to take one random example, one year after Haiti's 2010 earthquake, Haiti is still a complete basket case.
So, the Japanese earthquake has no doubt pricked your conscience. You have been reminded that there are people in faraway places who direly need assistance. Your moral intuitions are worthy, but if they lead you to donate money to Japanese relief, then you are probably doing something non-optimal from the point of view of improving human welfare. Donate, instead, to an international relief organization that consistently directs its efforts to the most needy worldwide: Oxfam International, Unicef, etc. It is even possible that these organizations will spend some of their resources to help Japan now; but they're in a much better position to analyze the situation and direct the appropriate quantity of resources in that direction than you are.
Accordingly, I just donated to Oxfam, and I urge you to do the same.
On the other hand, of course there are some forms of aid specific to the immediate aftermath of natural disasters for which money is not a substitute. Obama has directed the U.S. Navy to station aircraft carriers in Japan to help airlift relief supplies and such. Google has launched the People Finder for Japan. Etc. These organizations are uniquely situated to help in ways that no amount of money can purchase on the open market. And if you know of some similarly specific aid effort for which equivalents cannot be obtained via market mechanisms, then you should support that effort however you can.
A final caveat is that resources within Japan are unequally distributed. There are usually some very poor and miserable people even within rich societies. If you know of some specific subgroup within Japan which is unlikely to receive assistance due to the structure of Japanese society, then again go ahead and donate to help them as well.
But to a first approximation, the logical response to natural disasters in wealthy countries is to donate money to aid organizations generally, not to donate to aid for those countries. And yes, when The Big One hits the Bay Area (where I currently live), I'll say the same thing.