Do I need to reserve a seat on the train? How can I make a seat reservation?

DO ALL TRAINS HAVE RESERVED SEATS?
Often, trains have some cars dedicated to reserved seats ('shitei-seki'), whilst others are dedicated to unreserved seats ('jiyu-seki'). This is the case for Shinkansen trains.
However, most local trains don't have reserved seats, whereas other trains like the Narita Express only have reserved seats. (This doesn't mean that you need to book in advance but only that, when you buy your ticket, you will be assigned a specific seat number).

WHY SHOULD I BOOK?
If you are not catching the Shinkansen during peak commuter hours (between 7am and 9am or 6pm-8pm) or during national holidays, you shouldn't need to book your seat and you can use any non-reserved seat just by showing your Japan Rail Pass.
In fact, the Shinkansen trains run very frequently (at least every 30 minutes), particularly on the Tokaido line, between Tokyo and Kyoto, so you don’t have to worry about booking.
However, a seat reservation near the luggage area will be required in the Tokaido, Sanyo and Kyushu lines if the sum of the dimensions of your luggage exceeds 160cm.

HOW CAN I BOOK A SEAT?
If you want to book a seat you can do so without additional charges before you catch your train by going into a JR ticket office at the train station (also called a "midori no madoguchi") and showing your Japan Rail Pass.Japan Rail Pass holders can also reserve their seats for free at automatic ticket machines by scanning the QR code on their pass.