Easy Rupees At Dragon Roost Island:

After you get the Bomb Pouch (which makes it easier) go to Dragon Roost Island. Go to the part of the island near the Wind Shrine and bomb the large rock there. Drop down the hole that is revealed and complete the simple puzzle of defeating enemies. Your prize for completing this is 50 rupees. However, many jars are also in there, containing another 40 rupees that regenerate every time you enter that room. In about twenty minutes, you can have about 750 rupees easily.