Unlike, say, the UK, you normally get no discount for booking in advance, and base ticket prices are based strictly on distance, unless you're on a shuuyuuken (limited-time regional pass of the sort available to residents of Japan).

If you're going on local trains, for example, there is no price advantage in buying a through-ticket from Point A to Point C over buying a ticket from Point A to Point B and then another ticket from Point B to Point C. The class-of-service charge wipes out most savings on non-ordinary trains, however.