Japan may have more infrastructure and better disaster preparedness than Haiti, but they have the double problem of making sure people’s needs are met and preventing nuclear meltdowns at reactors that were hit. So if you have what to give, please read this page for donation options.
According to news sources, giving to the more established and reputable organizations will do the most good because they are already there and were ready. Still, if you have friends or relatives living or stationed in Japan, you can do a lot of good by sending them money and care packages to give directly to people whose lives have been impacted. Some may be hosting friends or relatives, and any little bit helps.