The List of Trains (Private and Public Train Operators)
See How to Read for the meanings of two-alphabet categories. This list includes retired trains which were withdrawn after 2010, but does not cover all rolling stock. Trains of Saitama Railway, Toyo Rapid Railway and Yokohama Minatomirai Railway (Minatomirai Line) are included in Tokyo Metro and Tokyu respectively.
The list of JR trains can be found HERE