Now a days you can check the timetables online or by the applications but it is much convenient to have a published timetable with you if you travel in Japan.
Online or applications are great if you travel from point A to point B but if you want to travel multiple destinations, it is difficult for example most of the online system will show you NOZOMI trains which you cannot take it if you are Japan Rail Pass holder!
Not like timetables are issued by railway companies in Europe, several private publishers in Japan issue their timetable each month. Although JR has its own timetables, I prefer to use JTB Publishing's one, which is elder than JR's.
Then, this timetable is great if you can read and understand Japanese.
Not only covering all JR trains(with some exceptions as like Yamanote line), but also domestic long distance bus routes, domestic and international flights/ships/ferries are written too. Also, private railway companies limited expresses and airport buses are mentioned too. Then, you can check the timetables and fares of the local buses which connect train stations and bus stops near the tourist attractions.
I hope one day JTB Publishing will issue an English version for tourists!