Boso View Express, or BVE for short, is one of those train simulators that have been around for a very long time but never quite managed to establish themselves at the top of the food chain, at least not here in the west. But if you want to simulate Japanese railways, BVE is essentially the holy grail.
You can find a huge variety of routes and vehicles, all of them with appropriate train protection and signalling systems courtesy of a highly-flexible plugin interface, for absolutely no money at all, but there is a downside: Basically the entire community is based in Japan, communicates in Japanese, and works on Japanese computers - which makes it difficult to get into the sim, or even to get it working, if you are not able to read and understand at least a bit of Japanese. (Google Translate, while definitely useful, often chokes on technical jargon.)
This guide aims to help you install the sim and addons, understand principles of how Japanese railways generally are operated and how they differ from what we Westerners would expect, and also point you to some up-to-date, high-quality add-ons.