Known to foreigners as the bullet train, as of last spring the Shinkansen (literally, "new trunk line") runs all the way from Kagoshima in southern Kyushu to Hachinohe, near the northern tip of Honshu. It's hands down the most convenient way to get between cities on any given line: door-to-door, it beats most flights, and the stations are a lot closer to town. As for driving, it's not even close: 8.5 hours on the road, versus less than 3 on the train, and not a whole lot of savings after you pay those astronomical Japanese highway tolls.
Plus, it's an awesome machine.
Check out these videos of how swift and smooth they are pulling in and out of the station. (Remember, e-mail subscribers - for videos, you need to click through to the blog.)