There are two ways to get full rupees, one only works for color:
In key caverns when you get to the boss slime eyes, do not ram the wall and hit him down, first kill the gels that fall from the ceiling until you get 999 rupees(they will move torwards you so equip the sheild and sword and stay on the side of the wall and they won't fall on you)

COLOR ONLY:
In the color dungeon, from the entrance, go up one room after moving the gaurds, right one room, and blow up the south wall and there will be green rupees all over the floor which are each worth five and there are almost 999, then leave the dungeon and come back and the room will be filled again and you can fill up rupees completely(so it's pretty much infininte rupees with no work or cost except for a 10 ruppe cost for the bombs

THE power of color:
When you beat the color dungeon boss a room will open to the right and you can chose a red shirt for offense power or a blue shirt for defensive power... you can always go back without facing the boss or mini-bosses to change shirt color. YOU CAN NEVER GO BACK TO GREEN (NORMAL)