You can quickly max out your Rupees to 99 extremely early in the game; to buy the Kokiri Shield, for instance. Once you are searching for the sword and preparing to by the shield at the beginning of the game, head over to the shop. Near the shop there are three man-made square blocks. From the shop side, jump over all three of them without falling into the water. You will be given 5 Rupees. Go into the shop, exit, and do it again. Do this over and over again until you max out your Rupees.