Originally Posted by
Ryvyan
My friend said that the Metro is the cheapest
Actually, JR is slightly cheaper than Tokyo Metro, which is in turn slightly cheaper than the Toei subway. JR fares start at 130 yen, Metro fares start at 160 and Toei fares start at 170.
In the Osaka/Kobe/Kyoto region, the cheapest train is usually Hankyu, followed by JR and the Osaka subway (which cost about the same as each other, but are quite a bit more expensive than JR and Metro in the Tokyo region).