Different cities in Japan have different charge cards for their transport. The charge card can be used to buy things from convenience stores, buy food/drinks from fast food restaurants and vending machines, pay for lockers in the stations, and of course to pay for transportation.
Osaka uses a charge card called ICOCA. Tokyo uses either PASMO or SUICA. They all effectively are the same except for the company in charge of it. For the whole of my Japan trip, beside using the Japan Rail Pass, I also used the ICOCA in Osaka and the SUICA in Tokyo.
Things to note about the cards is that most of them require 2000yen to purchase it at first. 500yen is the deposit for the card, and 1500yen is the original stored value. Then if you want the refund of the money, you need to pay a certain amount of handling fee to do that. Expiry date of the cards are 10 years from the last charge of funds. If you feel that in the next 10 years, you won't be going back to Japan, then definitely get your refund.
You can use the ticket machine at the stations to check on your transactions, and even print out a list of transactions from the machine. Can Singapore's MRT ticket machines do that?