I seem to remember a post a while back about diagramming complex routes. There is a thread in General Trainz that mentions a site hosting a free Railway Operations Simulator. It allows you to build a map of your route, set timetables, and operate it. The program is here.
I just used it to create a little spur off a main line. It took me ten minutes. The program also runs on LINUX under Wine (which is what I normally run).
Not quite on topic, but highly useful for those with huge routes.
Bill
Nice so It is a sort of network simulator. Looks a bit like software like Bahn only the layout shown on the picture on the page looks a bit more what a professional dispatcher would see.
There's also "Train Director 3", a very similar program based on the Italian ACEI signalling control system.
Compared to Railway Operation Simulator, it's actually easier but more realistic. Furthemore, among the downloadable routes there are three Japanese ones: the Seibu Ikebukuro Line (and related branchlines), the TRTA/Tokyo Metro Marunouchi Line and the JR Tsurumi Line.
Here's a screenshot of the Seibu Ikebukuro Line map: