Here is a list of some small Japanese railway museums that are known about at the end of 2009 (there are others) - with some later additions .
Shiga on Lake Biwa near Maibara - 1882 station and loco D51-793 and an ED70
Karuizawa, KIta-Saku, Nagano - electric 10000 and EF63-2
Engine shed, Hisatsu-sen, Kyushu, loco D51-170
Fukuchiyama, Kyoto, loco C58-56
Old Station at Atsushio, Kitakata City, Fukushima
Misaki, Okayama. Units and Line
Agematsu, Kiso, Nagano - sightseeing railway
Kyushu, loco 59684 - plus other mining musuems nearby
engine shed with D51-170
Tobu Dobutsu Koen station, Saitama, loco 2109 and shed. TripAdvisor
Tram line and steam line at Inuyama, Aichi
Tomisawa, Taihaku-ku, Sendai - trams
Established in June 1994 to celebrate the 100-year anniversary of Meitetsu (Nagoya Railroad).
Iyo Saijo, Yosan linbe, Shikoku - DF50-1, Shinkansen car
Horonai/Mikasa S-304, C12-2, 59609
Asahikawa, Hokkaido - station and 29638, C57-201, D51-6
Obohro, Hokkaido - station and railcars
Steam loco 49643, carriage and small museum. Japanese Wiki
The O-Yubari line museum closed in 2008, but still houses items (eg D51-101 and Yubari 14). Local rail fans restoring old coaches at Minami-O-Yubari station site (open May-November, with a festival in September).