The ride from Shimane Masuda to Yamaguchi is particularly nice. The small hamlet of Tsuwano is located on this line and quite nice to walk around.
The last stretch from Hashimoto up to Koya San is very pretty. But this is on the Nankai Line which the Railpass will not cover.
The Enoden from Kamakura to Enoshima is very picturesque and this narrow gauge winds along residential areas and seaside. This is also a private line.