While darting around the country on the shinkansen, Japan's highly efficient system of bullet trains, might be practical and time-saving, whizzing through the countryside at over 300 kilometers per hour doesn't really allow you to see much in terms of scenery. However there are numerous train lines around the country that leisurely make their way through Japan's beautiful rural scenic routes. On these train routes, it's the journey itself that is an attraction.
Kurobe Gorge Railway
Traversing deep into the Japanese Alps, almost the whole stretch of this railroad is accompanied by gorgeous scenic vistas. To allow passengers to appreciate the beautiful mountain scenery even better, most of the train even features open-car carriages which adds to the natural atmosphere. The train starts at Unazuki Station in Toyama Prefecture and takes about 80 minutes to get to the last station at Keyakidaira.
Gono Line
Running along Japan's far northern coast between Aomori and Akita, the Gono Line travels along a region that's hardly explored by tourists. Get on one of the Resort Shirakami trains and you'll even be treated to traditional music performances to complement the incredible coastal views. The train line takes about five hours in total but is well worth it and there are numerous places you can stop and explore on the way.
Tadami Line
Fukushima's Tadami Line takes passengers through stunning mountain scenery, dramatic gorges and valleys as they make their way to neighboring Niigata Prefecture. With a number of fascinating stops along the way, make sure to pay a visit to Mishima Town, one of the most beautiful villages in Japan. Note that the section between Aizu-Kawaguchi and Tadami Station is still closed after severe damage in 2011, instead there are buses scheduled to take train passengers between this section.
Hisatsu Line
On Japan's southern island of Kyushu, the Hisatsu Line travels between Yatsushiro in Kumamoto and Kirishima in Kagoshima, traversing into the mountains between the two cities. For a really memorable experience you can also ride a steam train, the SL Hitoyoshi, that travels on the same track, although you'll need to book in advance.
Sagano Scenic Railway
For those taking Kyoto's Sagano Scenic Railway, it doesn't really matter where you end up, the attraction is all about the journey itself. The train trundles gracefully through dense forest following the Oi River and its picturesque valley scenery. The railway is most popular during the autumn season, when foliage turns to beautiful shades of red, orange and yellow. If you're planning on visiting during the winter, be aware that the railway doesn't run from December 31st to the end of February. It also closes on most Wednesdays of the year.
Hakone Tozan Line
Traveling through one of Japan's most beloved national parks, the Hakone Tozan Line climbs up over 500 meters into the mountains of Fuji Hakone Izu National Park, in the shadow of the impressive Mount Fuji. Hidden within the valleys of the park you'll find some of the country's most beautiful traditional hot springs known as onsen, many of which are easy to reach from the train stations. Currently a section of the railway is undergoing repairs after a recent typhoon, so make sure to check if it's operational yet beforehand.
Takayama Main Line
The main line that travels through the mountainous prefecture of Gifu, the Takayama Line passes through a number of the region's important attractions such as Gero Onsen, Takayama City and Hida before finishing at the coastal city of Toyama. On the way you're treated to beautiful scenic views out of the train's window. Make sure to take the 'Wide View Hida' train which runs along the line, it's fitted with extra large windows which make gazing out into the picturesque countryside much more impressive.
Conclusion
While most routes of the shinkansen don't really allow for much gazing out the window at beautiful scenery, if you're traveling from Tokyo to Nagoya or Osaka, you can often get a glimpse of the iconic Mount Fuji as long as the weather is clear enough. Sit on the right side of the train if you're heading south from Tokyo or on the left if you're going north towards Tokyo.