Golden Rupees

Go to the Lost Woods and find the Skull Kid who is alone as adult Link. Then, lock onto and kill him, and he will give you a golden rupee after he's dead you can do this as many times a you want.

After collecting 100 gold skulltulas you can go into the house of skulltula talk to the guy and he will give you a golden rupee, everytime you stop in.

in the fire temple above the boulder maze.

use the lens of truth just after you get it from the bottom of the well to see a hidden chest with a golden ruppee.

In the gerudo training grounds the closest, like like chest in the end of the left trial rooms.