Just one screen to the right of the Desert in the Light World, there is a passageway under a giant rock that leads to a room, that has a total of 50 Rupees under pots.
You can just keep entering and exiting and collect the Rupees every time.
Also, in the Dark World, if you're skilled enough with the bow and arrow, you can play the archery game for 20 Rupees, (south of the Village of Outcasts) and get rupees fast that way. If you hit 5 for 5, you'll get 4+8+16+32+64=124 Rupees (104 Rupees after subtracting the 20 used to play the game)
--- "Er...well, y'know. You can't make an omelette without um...destroying a forest.....or something" -Black Mage