Realrailway.com
they have more then one train and it kind of reminds me of tain simulator+densha de go!
as far as i can tell its not very detailed but still fun to mess around with.
train lines that are there are:
Shinjuku Line
Sotetsu Line
Ikebukuro Line
Enoshima Line
Inokashira Line
Chitose Line
Keio Line
PS sorry if i misspelled any of the line names!