Purchase something big (The Bow - 980 rupees). Give it to the clerk, and as soon as the text box disappears (saying you got the bow), and before all of your rupees decrease, bring up the save screen and Save & Quit. Restart the game and select the file you saved. You will have most of you rupees still (depending on how low the rupee counter was when you saved it).
Submitted by: Richie Sauer