CharityNavigator first, a site that vets the effectiveness of various charitable organizations.
At this point, the State Department of the United States (as well as the UK's Foreign and Commenwealth Office and Australia's Department of Foreign Affairs and Trade) is urging all travelers to delay non-essential travel to Japan, even to those areas that have been only minimally affected by the quakes, tsunami and nuclear reactor issues (like Tokyo and Kyoto). Most airlines are allowing passengers to change their tickets for travel in the near future for free, but policies vary, so do check with your airline for complete information.
As for transportation options, the major international airports are now operational again. Trains are running in many areas; an English-language website has been set up by volunteers to help travelers find which ones they can take (click here for that site).
For those trying to locate family, friends and travel companions, Google has set up a "people finder" site. You can click here to read CNN's article on that.
Yesterday on our radio show we interviewed Vikki Corliss of the insurance aggregator site InsureMyTrip.com and she assured me that the major insurance agencies have been working diligently to help their clients get out of Japan. All are honoring their policies, according to Corliss, since all travelers have experienced trip interruptions of more than six hours. Those currently in Japan without travel insurance should contact their embassy for assistance of call 0570 000 911, the number the Japanese government has set up to assist foreign nationals.
The picture is less clear for those hoping to cancel their trips to Japan in the coming weeks. Those who purchased "cancel for any reason" insurance policies should be okay. Others should contact the travel agencies or tour operators they've booked with; or their insurance agencies. to find out what their options are. As is usually the case in these disaster situations, policies are being created right now, and seem to be changing on a daily basis in response to events in Japan.
Update: Just a few minutes ago, General Tours announced it would be giving full refunds to any of its passengers scheduled to go to Japan in March. For those traveling in April, General Tours is allowing customers to either rebook Japanese tours for later in the year at no penalty; or switch to a tour to a different destination, again with no penalty.