Ok, here's the back-story from what I can piece together from Google Translate, assorted blogs, YouTube captions and one About.com article. (As ever, your better-informed input is appreciated.)
The opening of a new bullet train line in Japan was scheduled for March 12. This new line would connect two pre-existing lines, making it possible to high-speed the length of most of Japan. It's not actually called the Happy Train. The Japanese apparently pair the name of their high-speed rail system, Shinkansen, with the name of the line. In this case, Kyushu Shinkansen.
So it's a big deal for the country that this rail line is opening and they put out a call to the general public to participate in a new commercial by waving to the train as it makes a pass along the new route. At least 10,000 and maybe more than 15,000 people show up to wave and cheer and from what was shot from the train itself comes the video above.
The day before the line opened, March 11, the giant earthquake and tsunami struck. The celebrations were cancelled and the commercial (which either never aired or only aired a few times) was pulled.
The words at the end are reportedly, "On that day, you waved at us. Thank you. You smiled for us. Thank you. You came together as one for us. Thank you. From now, Japan is linked together, from top to bottom. From now, Japan will become fun."