In The Legend of Zelda: Ocarina of Time 3D for the Nintendo 3DS, there are a couple of methods you can use to essentially get an infinite amount of rupees any time you need them.
1. There is a beggar in Kakariko Village as an adult that will buy fish from you for 100 rupees each. Behind the potion shop in Kakariko Village is a Grotto with a fish in it. Bring some bottles and catch the fish. Go out of the Grotto and back in until you’ve filled them, and go back to the beggar to sell them to him.
2. As an adult, go to the Lost Woods and find the lone Skull Kid. Kill him, and he will give you 200 rupees. Go out and back into the area and he’ll be there again.