Someone made a list-> http://www.geocities.com/thetropics/...0/scenic2.html

Some of the routes I've taken are:

Tokaido line Odawara-Atami -- view of the Pacific Ocean
Tokaido Shinkansen near Mishima -- view of Mt Fuji (if the weather cooperates)
Iida line (Tenryu gorge) -- the tracks follow the scenic Tenryu gorge.
Oito line north of Matsumoto -- view of "Japan Alps".