Since my trip to Japan was relatively soon, and I needed to go from one international airport to my conference site on the way in and the way out, I started to look for Japan Rail Pass. The multi-day pass (7, 14, and 21 days are available) is expensive in the hundreds of dollar range (due to exchange rate fluactuations, the exact cost will change unless bought it using Japanese Yen) but worthwhile, since couple of trip in Shinkansen (Japanese Bullet trains) is costly. So even if you are going to be traveling two or three days and take long trips it is worthwhile to get the Japan Rail Pass.
First the traveler needs to determine whether he/she needs Superior Class (Green) or Ordinary Class (Pink). The Green pass is about 1 1/3 more expensive but there are certain advantages. Then the traveler needs (assuming it is an adult; if not there are children's passes available too) to decide whether she needs it for 7-, 14-, or 21-day validities.
Then he needs to decide whether he will be traveling more than one or two regions of Japan or will travel extensively in one region only (refer to www.japanrailpass.net/eng/en001.html for regions). Assuming she will travel more than one region (which is probably best bet if you are visiting Japan for a short trip) then go ahead decide on the General Pass rathern than Regional Pass.
I decided to go with the General Pass and so I contacted the travel agent to get the Rail Pass and purchased it. What I got was not really the Pass but receipt to purchase the Pass. Once you arrive in Japan take this receipt and passport and then you will get the real Pass at Exchange Office. At that time you have tell them when the start date and time of the pass will be. It Need NOT have to be immediately. However, once the start date and time is stamped it can't be changed. So plan ahead and get it stamped properly. Let us, say your first trip using the train will be a short one and you will not travel for another day or two. Then buy separate ticket for the short trip and save the pass for the extensive and long trips.