As I recall, one of the best ways to get rupees is to go out on a whim and begin the Savage Labyrinth [it's on Outset Island, there's a lone pillar where you have to lift up a Stonehead with Power Bracelets. After every (10?) floors, you get to a save room that features a pot full of [fairies + hearts?] and another full of rupees, of which featured are blue, red and obviously green. Just enter, defeat a couple enemies, get your rupees, exit. Takes little effort at all.