I think a lot of people are using Redcross as they are also based in Japan. I have seen their trucks on the news here delivering food and water to shelters so you can be sure that it's getting to the people it needs to. Here is a link to the Japanese Redcross society I used if anyone is interested.
http://www.jrc.or.jp/english/relief/..._00002070.html
You can donate to the Redcross in Canada, or with the info in this link you donate directly into one of their bank accounts based in Japan. I would assume by donating here the funds would be able to be used by them a lot quicker in the affected areas. I'm not really sure about some of the other organizations so I can't comment too much on them.
There are a lot of logistics problems now. Many roads are blocked by debris, rail lines aren't working in the area, and there is a shortage of gasoline for the delivery trucks. Part of what frustrates me about media just focusing on the nuclear plant is that the first week, and especially first 3-4 days are critical for rescuing people caught in a disaster like this. While some people were able to grab their earthquake kits and survival bags when they ran, many didn't have time. Many of the shelters are running out of water, food and medication - if they haven't already. Also anyone with a medical condition, like diabetes for example, doesn't have access to meds that they need. I also saw a clip on the news that a nasty influenza bug is affecting some of the shelters. One of these had only one doctor on hand for about 300 people, and many other shelters do not have anyone with medical expertise.
Some areas are also very difficult to reach because of Japan's mountainous geography. Some of these small towns have only one major exit through a valley, so if that gets blocked by massive debris or a landslide it makes it very difficult to get help there. The tempurature up north also dropped below zero again tonight and there is heavy snow in many areas. Most shelters do not have any basic utilities like water, power, heat, or working phone lines. So yeah, it was already unbelievably ugly before, but it's getting worse for many as they are running out of time. Many people are being helped and found, but the disaster area is so massive and absolute.
While its true Japan is a wealthy nation and will survive as a country long term, I don't think any wealthy nation in the world has the resources or personel to deal with something on this scale in the short amount of time needed to save lives. Hundreds of thousands of people lost their homes, businesses, friends, family in a short few hours. Entire towns, and large sections of cities are just completely gone. I personally don't think any amount of money will replace entire communities of people being wiped out. That is the real catastrophe. I can't imagine the feeling of having everyone I've ever known taken from me in a few minutes.