Hi Alan,
Having travelled with countless JR Pass, I can't live without making seat reservations. Having an assigned seat before boarding the train means you don't have to queue up on the platform beforehand, fight with other passengers and just gives you that peace of mind to make travelling an enjoyable experience.
That said, it is generally it is not required to make seat reservations as trains rarely sell out and you can just take a non-reserved seat if you like. There are a couple of exceptions:
During periods of national holiday: Golden Week (April 27th - May 6th), Obon (August 11th - 20th), New Year period (December 28th - January 6th). These days can vary a little depending on the year and how weekends fall.
Green Seats, all green seats need a reservation beforehand.
Some trains only have reserved seats. These are the Narita Express, the Hayabusa Shinkansen between Tokyo and Shin-Hakodate, the Kagayaki between Tokyo and Kanazawa.
Seat reservations are always free with the JR Pass and I suggest getting them :)
Also see our Blog Post on seat reservations.
Hope you find this useful.
-Daniel