Although you can check the timetable of trains by smartphones, paper timetable is still convenient to have when preparing your trip.
Still in 21st century, many paper timetables are published in Japan. There are many local ones or timetables for single railway operators and also nationwide timetables issued by several publishers. However, unfortunately all of them are in Japanese only.
What is the difference between Japanese and European paper timetables? The biggest difference is that Japanese one also covers airlines, ferries and buses. For example, you can check the timetables of Japan Airline divided by destinations. Also you can check the fares too.
Then, nationwide timetables are issued each month. Adding seasonal trains, flights, ferries and buses which are operating in coming month. Paper timetable may be worthless to carry during your journey but better than using smartphone's application when planning your journey.