A great way to accumulate rupees fairly quickly is to head to the Dee Ess Isle (which is an island on the map suspiciously shaped like a Nintendo DS Lite) once the Goron Game is available. Winning this game is easy once you've done it enough times, and going through the course given in thirty-five seconds will net you all sorts of goodies. Sometimes, you'll get 200 rupees as a reward, which is good enough, but you'll also sometimes get items, such as Zora's Scales (which you can sell for 800 rupees), or Coral (which you can sell for a whopping 1,500 rupees).