I have just used the JR pass web site to work out if it is cheaper to book our train journeys independently or use a JR pass.
It worked out it was cheaper to book the tickets individually as we also want to do some trips that the pass does not cover. After doing some research about booking the tickets in advance I understand that the JR pass does not have a reservation fee but to book each ticket individually does. So my question is, does the comparison on the web site include the booking fee for the individual tickets? Hope this makes sense!
Thank you!
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Whether the cost of reserving a seat is accounted for or not, it almost never makes a difference when working out the math to decide if a pass is better or not.
In fact, I make it a point not to account for the reserved seat fees, even though the pass being compared would include the benefit of seat reservations. It really offers perspective as to how much value the foreigner passes can pack.
So if the cost of individual tickets isn't anywhere close to the cost of the JR Pass + cost of trips that the pass does not cover, you should forget about the pass.
You don't list your itinerary so I can't say which is the better way. If you want, there is a simple calculator you can use at:
http://www.japan-guide.com/railpass/
For all the routes, fares, and schedules, there is Hyperdia:
http://www.hyperdia.com
You will get 2 listings on Hyperdia - one is the base fare, and the other is the seat fee. You must include both for the total fare. For some trains like limited express and bullet trains, there are also in addition advanced seat reservations you can choose as an option. For regular tickets, there is an extra cost, but advanced seat reservations are a free perk if you have the JR Pass.
Most of the time you don't need advanced seat reservations and you can just grab a seat in the Unreserved cars of the train. So the above is correct - you really don't need to include the extra reservations charge in calculating the total cost. A few trains like the Narita Express and a few bullet trains only have advanced seating though. You should calculate it yourself in any case - another pass seller (not this one) always slickly adds the advanced seat fee in the total to bias the results and sell more passes.
There is no ticket booking fee, unless you are going through a 3rd party to buy the tickets for you.
If in fact the full JR Pass does not pay off for you, it may be that a regional pass might save you some money. Have a look at them at:
http://www.japan-guide.com/e/e2357.html