It's better if you do this at night and slow down time. Simply enter the goron race. If you win, you will be given some gold dust. Keep racing until all your bottles are filled with gold dust. When they are, go to the Curiosity Shop in West Clock Town (opens at 10pm) and sell the gold dust for 200 rupees each. Since the bank is right outside the Curiosity Shop, you can easily put the money in your bank. If you have the giant's wallet, sell them by twos so you will get 400 rupees, put that in the bank, then sell two more, etc.

2.Break the pots

This one is sorta easy once you get used to it. I've done it over 6 times in a row. The requirements for this are:

To do this, you must go to the Great Bay (the half where Zora's Domain is located) During the DAY (won't work at night). You should see five pots ontop of rocks. I'm pretty sure everyone knows that you're supposed to try to break all of them. Now, for the position. Position yourself so that your back is facing the water where Zora's Domain is, and you're looking at the center of the pots. Step back so that you are next to the Zora that tells you you have to pay 10 rupees when you break a pot (the one that's farther back). Step slightly back (2 or 3 steps) and take out your boomerangs. Aim right at the middle. If your boomerangs came back too early to reach the pots in the back move a little closer. If they went too far and went past the pots then move back. When you get all the pots you should be awarded with 90 rupees (or piece of heart if it was your first time). Take about 2 steps backwards and do it again. Keep doing this and go back to the bank to save the money.

3.Bugs

To me, this is a slow way to do this, but I've done this in OoT too. Requirements are:

This is fairly simple but can get boring. Go to the Stock Pot Inn. Go upstairs to the room where Guro-Guro is (or where the two brothers are playing cards at night). Catch a bug in a bottle. Release the bug in the bottle and three should come out. Catch as many as you can and keep multiplying them. Sell them at the Curiosity Shop after 10pm.

4.Various Rupees in Town

This won't get you 5,499 rupees right away, but if you do this every time you go back in time it will eventually pay off. For this you must have the following requirements:

There are lots of places in Clock Town that give you rupees. Here's a list of them in an order that would make it the easiest.

If you have the bunny hood, put it on and go to east Clock Town. Go outside the mayors office and follow the stairs to the roof of the milk bar. On the side where the guard is, jump off the roof onto the target where Honey & Darling's minigame place is. Jump off of that target onto the next one (if you land in the basket that's ok, you can jump out). Jump off that target and go onto the roof of the shooting gallery. Climb up the short ledge infront of you and you will be in a wood area with a chest. The chest has 100 rupees.

After you get the chest, do things like shoot the targets infront of the shooting gallery and Honey & Darling's place, or throw a bomb in the basket infront of Honey & Darling's minigame place. You will get a few rupees.

Go to West Clock and buy a lottery ticket. IF YOU DON'T KNOW THE NUMBER, WAIT UNTIL IT IS CALLED AT NIGHT AND WRITE IT DOWN. The Lottery number is always the same when you go back in time. If you know the number, enter it.

Wait for the mailman to deliver the letter to Anju in the Stock Pot Inn (I think it's at 2:30pm). Then talk to her while wearing the Kafei's Mask. She will tell you to meet her at 11:00pm.

Take off the Kafei's Mask and say you have a reservation. She will give you the keys to a room upstairs. Go up into your room and you will find a chest with 100 rupees.

Go outside Clock Town on the Snowhead side of Termina. Somewhere in the area with the frozen trees you will find a wall with some notes on it (sometimes they're songs from OoT :P). Simply stand infront of it and play the notes and rupees will pop out.

(Skip this if you DON'T know the lottery numbers) Play the Song of Double Time (right, right, A, A, down, down) and go to West Clock Town. Go to the lottery place and claim your prize.

Wait until 12:00pm and go to the kitchen in the Stock Pot Inn (she's an hour late >:( ). Talk to Anju and mail the letter she gives you.

On the next day, wait until the Postman delivers the mail. He should go to the laundry pool. Go inside the door and talk to Kafei. He will give you a necklace to give to Anju. Go to the Stock Pot Inn and show it to her. Now, go to the Post Office. Put on the bunny hood and keep playing that “wait 10 seconds and then hit A” game. You should get some rupees off of that.

Again, if you know the lottery numbers enter them and get the prize the next day.

On the third day, there isn’t much to do. You can play games such as the shooting gallery or Honey & Darlings minigame of the day.

When it is night of the Third day, go into the Stock Pot Inn (even if you didn’t help Kafei get the sun’s mask) and go to the room upstairs where Anju is. There should be a treasure chest there. Open it for 100 more rupees.

5.Curiosity

Sell pretty much anything you ever get in an empty bottle at the curiosity shop. I even sold the seven Zora Eggs for 20 rupees each XD

There are lots of ways to make money in Majora’s Mask. These are just a few… You can do other things such as play non-stop minigames, or something like that.