By far, I've found this to be the single best method for Rupees in MM:
Note: The Bunny Hood is not required, but is strongly recommended.
North of Clock Town are groups of Dodongos. Dodongos drop a Purple Rupee (50) every time you kill one, and are a very easy source of money -- the problem is, there are very few Dodongos around, and they're not very easy to kill. The problem is that Dodongos do a tail swipe that spins them around, inflicting easy damage on you and moving their weak spot away from you; however, this is easily remedied if you do it properly.
Try using this method: Approach a Dodongo from behind, and have Z-Targeting off. Hold out your shield and press the B button as fast as you can, stabbing the Dodongo in the tail, causing it to flinch. If your shield is out, you will block the tail swipe and take no damage, but it's even better if you can cause the Dodongo to flinch infinitely by timing your sword stabs such that the Dodongo is always being hit with your sword, and therefore can't start to do a tail swipe. The timing is much more easily perfected with the Bunny Hood, and if you time it right, you will kill the Dodongo very quickly without it spinning and without you taking any damage. You now have 50 Rupees.
Want more? There is a bomb-able rock near where the Dodongos spawn, and underneath it is a hole. Inside the hole are two more Dodongos that can be easily dispatched with the same method. Once you exit the hole, the Dodongos in Termina Field will respawn and can be killed again easily with the same method for more Purple Rupees. Keep going in and out of the hole and killing Dodongos until your wallet is full. You can make 500 rupees easily in a little under five minutes.
Simply head on down back to Clock Town to deposit the money from your full wallet and repeat as necessary.