Don't wait untill you have 100 Gold Skulltulas to get the golden Ruppee, get it as soon as you get bombs. As either Link, go to Kakariko Village. Right when you walk in there is that tree in the middle. Well take about 10 paces directly behind that tree, you should be in the center of a somewhat open area in the town. (If you have the Stone of Agony, you will feel it rumble.)

Place a bomb there and back away, when it explodes there will be a hole in the ground and kill the two mummies with the Song of the Sun and your sword. A treasure chest will appear with a golden ruppee inside.