The way I always rack up money is:
1.) Make sure you have Gibdo Mask and teleport access to Ikana Canyon.
2.) Equip Gibdo Mask and run to Redead room in the castle.
3.) Kill all Redeads (they will be dancing if you still have mask on), collect rupees (each one drops 15-20 rupees).
4.) Go out, go back in, kill again.
5.) Do 3-4 until wallet is full. Once wallet is full, teleport to Clocktown, deposit rupees in bank, teleport back to Ikana Canyon.
6.) Repeat 1-5 until desired amount of money is obtained.
I always do this to get the heart piece for depositing 5000 rupees in the bank. Last time I did it, I had the Gilded Sword, so the Redeads dropped rather fast each time. But it's easy enough without the Gilded Sword, too. They don't attack, making it a really fast and easy way to get money at this point in the game. It takes a little time, but is worth it in the long-run, and the quickest way to earn money that I know of.