Understanding JR/hyperdia fares
 

How can you tell when searching JR fares on hyperdia whether it is mandatory to pay the extra charge for a reserved seat, or if you can get away with just paying the base fare?

If you have a jr pass then you don't have to pay the reserve seat price.

If you are just buying a ticket then you also pay the reserve seat price to reserve a seat along with the price of the ticket.

If you don't pay the reserve seat price while buying a ticket I believe you can still stand on the train with no seat in the back of the cars.

Aloha!

sorry, just reread your question.

If it has reserved seat charge listed next to your train schedule that usually means that all seats on that train are reserved and you have to pay the reserve seat price to get a seat on that train.

Aloha!

The "reserved seat charge" listed on hyperdia is more than just that. It is the cost of an reserved seat (only 500 yen or so and your option) plus a mandatory limited express surcharge.

See this:
http://www.japan-guide.com/e/e2359_001.html

Go to hyperdia and do a search for Kyoto to Shinosaka, departing at 11AM, and you will see the range of fares: Nozomi shinkansen, Hikari shinkansen, Thunderbird L'Ex, and a JR Rapid train (the rapid train is a local with fewer stops).

See the base fare is the same on all the trains: 540Y.

The difference between the two type of shinkansen fares is the mandatory 200 yen extra fee paid, in season, on the Nozomi.

So, for trains that have a reserved seat charge on hyperdia you can subtract 500 yen from the "Total amount of money" to see what you'd pay to go without a reserved seat.

Base fare is the cost from point to point using local trains which take time, lots of time, as they stop everywhere. They are also not comfortable, usually with wooden bench seats along the side or simple plastic seats...kind of like subway.

When you use anything but local trains, you pay the charge for the upgrade in speed and comfort. That charge is listed under the column CHARGE. If before you search, you choose unreserved seat, then the small charge for a seat reservation will not be included. There is no reason not to get a reserved seat if they are available, as their cost is only around ¥500 as mrwnrfl explained, and they can save you a lot of hassle waiting on line for unreserved cars or scrambling for unreserved seats.