First, beware of scams. Many NGO's (non-governmental organizations) may claim to help Japan. Check to see if they are legit organizations by checking them out on these two websites:
Charity Navigator (their website is down at the time of this posting, but keep checking back)
These are two sites in which you can type a charity's name and see where they work, and how they are rated in donor efficiency.
Beware of phone calls from organizations purporting to be with a legit. charity. Ask for the name of the charity and call the charity's regular phone number to check and make sure it's not a scam. Also, I'd avoid giving to anyone collecting money on street corners. Yout cannot be sure where the money is going. If a friend or group is organizing a drive, that's different.
Here are some links on good articles on giving to Japan.
How to avoid charity scams
How to help Japan
PART TWO: What's needed?
After a catastrophe such as an earthquake, victims need food, water, blankets, tents, generators, temporary shelters, tarps, medical assistance and much more. It's best to give to an organization that is either sending these items or better yet, is already on the ground and stands ready to help.
Do not give old clothing! It only clogs up the warehouses for the more important items needed by victims.
After the Haiti earthquake, I went to a large staging compound where many NGO's were forming teams to help. We had donated a 10,000 gallon water purification unit to The Red Cross and wanted to see how it was functioning. Teams were going out into various areas and assessing needs of victims. The strongest needs where at the time for clean water, medical help, food, and shelter. But larger items to AID these organizations were also needed... such as generators, gasoline, etc. These too, are important.
PART THREE: Whom to give to?
These are organizations that say they are helping. You may check them out on Guidestar or Charity Navigator.
The Red Cross (you can text the word REDCROSS to 90999 to donate $10 to relief efforts. The charge is added to your cell bill). Personally, I'd rather send in a check and write in the memo: JAPAN RELIEF ONLY because this earmarks the money. I like the Red Cross, I've seen what good they do in disasters, but they are a large organization helping many countries and you want your donation to help the afflicted country). Visit this link to donate online directly to Japan. You are giving to the American Red Cross, but they are saying they are in direct contact with the Japanese Red Cross to see how they can help.
Here is a link, translated, to the JAPANESE Red Cross, for anyone interested.
One of my personal favs is Doctors without Borders (I saw the amazing work they did in Haiti). They have teams trying to reach the hardest-hit areas in Japan. Here is their Guidestar report; they come highly recommended.
I'm sure other charities are mobilizing and seeing how they can help. Again, check them out with Guidestar or Charity Navigator before donating.
Good luck and thanks for helping! I'm leaving for Honduras for the day job and will be offline, as we will be in very remote, very poor areas. Please keep the people of Japan in your thoughts and prayers.