The Legend of Zelda: Majora's Mask/Secrets

Zora Pot-Breaking
Unconfirmed if this is 3DS only. As Zora-Link, go to the pot breaking game (open during the day) on the West side of the Zora Cape Area. If you stand against the wall directly behind the middle pot and aim directly at it, you should be able to break all five pots with one shot from the arm boomerangs. This will net you 90 rupees each time. You can repeat immediately for the same result. Once you've found the right spot you won't even have to move Link to continue making the shot. This is probably quicker than the Takkuri method and doesn't involve using any consumables or risking anything (10 rupees are taken per miss if you have them. Otherwise it's free). Just warp back to Clock Town, deposit your cash and then warp to the Great Bay Coast (it's faster to get to the mini-game than warping directly to Zora Cape as the pots are located right next to the entrance from Great Bay Coast).

Takkuri
Head to the portion of Termina Field by Milk Road. Here, you'll find that really annoying bird that flies at you and steals your stuff. If anything important gets stolen from you, either go buy it back at the Curiosity Shop or play the Song of Time. If you feel apprehensive about facing this thief-bird, put on the Stone Mask so he doesn't try to steal from you, but it's easier to hit him when he's flying at you instead of in random circles. Alternatively, take out Takkuri using your arrows while mounted on Epona - the bird cannot steal anything or hurt you while on Epona.

Pull out your bow and shoot Takkuri until he dies (Light Arrows work well). When his body drifts to the ground, it will yield a huge rupee - 200 big ones! Now just head through the loading zone into Milk Road and back and do it all again! Have fun. This is the fastest way to get money, and consequently, the Piece of Heart for having 5,000 Rupees in the bank.

Blue Bubbles
These can be found in the Stone Tower Temple or along the road to Ikana (and a few up the road to the Ikana Graveyard as well). Hit one with a Light Arrow to receive the substantial reward of a Purple Rupee. Not bad for one arrow's work!

Dodongos
These dinosaurs can be found in Termina Field outside of the road to the Mountain Village. Kill an adult for a Purple Rupee, the one smaller one for a Red Rupee, and drop down the hole next to the smaller one to find two more adults.

Clock Town
Even though the Takuri Rupees make all other get-rich-quick schemes obsolete, there are other ways to get relatively quick money:

East Clock Town
There are two treasure chests each containing Silver Rupees: One of them is down in the Bomber's hideout. Down the ramp and to the left when you get to the water. Pull yourself out of the water at the end and blast the wall with either a bomb, bombchu or the Blast Mask (use your shield while you blast to protect yourself from harm). Open the chest to receive a Silver Rupee (100). When you come out of the Bomber's hideout, hang a left and run along the left wall, hopping over gaps (use the nest outside Honey and Darling's Shop as a jump-off). When you get to the far corner, turn right and head to the chest. Open it to receive your reward.

You can also play at Honey and Darling's game place on the First and Second Days to win a Purple Rupee (50) if you score a Perfect. On the Final Day you get a Piece of Heart. If you didn't score a Perfect on both the First and Second Days, you can only win a Purple Rupee on the Final Day. After you get the Piece of Heart, any more winnings will only win you Purple Rupees.

If you like to use your bow, then the Town Shooting Gallery is the place for you to be. It puts a little more challenge into getting your money, but its rewards are greater than any other mini-game. The first two times you score a Perfect, you win a larger quiver and a Piece of Heart. After that, wins will get you Gold Rupees (200). Please note that you can play this game as often as you like, since it doesn't require you to win all three days.

The only real reason you'd want to go to the Treasure Chest Shop is to get a Piece of Heart, but it is possible to get monetary rewards as well. You can play the game in all four of your shapes (Link, Deku, Goron and Zora); however, each shape costs different amounts to play and have different rewards. Pay 30 Rupees and win the game once as a Goron to get a Piece of Heart. After that, winning as a Goron will get you a Purple Rupee; as a Zora, pay 5 Rupees and win a Red Rupee; as a Deku, pay 10 Rupees and win one Deku Nut; and as Link, pay 20 Rupees and win a Purple Rupee.

If you make a reservation in "The Stock Pot Inn", upstairs the second room on the right hand side, open the treasure chest and you will find a silver rupee worth 100 rupees.

After the time changes to "Night of the Third Day", you can run to the Stockpot Inn. Atop the stairs, the room that is usually locked, is now unlocked. Enter and you'll be in Anju's room. She has fled Clock Town but her chest still has a silver rupee worth 100 rupees. You can then hurry to the bank and deposit that. Then you can reset time or go fight the Skull Kid. This works as Link or when you're stuck as Deku Link. It can be repeated every "Night of the Third Day" also. With the purple rupee atop the Festival Tower and Anju's abandoned silver rupee, you can get 150 rupees in every three day cycle.

North Clock Town
Pretty much all there is to do here is the Deku game. As a Deku Scrub, burrow into the flower next to the Great Fairy's cave and launch yourself into the fenced-in area. Drop down the hole and participate in the game. The object of the game is to collect all of the rupees by launching yourself out of the Deku Flowers onto other platforms, but you may not touch the ground. If you win the game on the First and Second Days, you get Purple Rupees and on the Final Day you get a Piece of Heart. After you win the Piece of Heart, any wins will only get you Purple Rupees.

West Clock Town
Though the reward is not worth the effort at all, you do receive monetary rewards from the Mighty Training Center. Take the Expert Level Challenge. Jump attack all ten poles that appear, and you will receive a Red Rupee (20)! Yipee!

NOTE: The first time you successfully hit 30 points, you will receive a Piece of Heart.

South Clock Town
On the Final Day, obtain the Land Title Deed from the Deku Scrub by trading him the Moon's Tear. Use that to fly to the platform with the chest on it (opposite the Clock Tower). Open that chest to receive a Purple Rupee. Alternately, use the hookshot. Also, in the Laundry Pool where Guru-Guru usually sits, there is a box right beside it. There is a single blue rupee in it. But, like using the Postman's Hat, you can keep doing it over and over. You just have to leave and come back. It's tedious, but if you have a lot of time on your hands, and you're patient, you can get enough to fill you wallet and then some!

Mail Money
Postman's Hat required. Wear the postman's hat and check any mailbox to receive free rupees. most of the time you will only get one, but in north and east clock town you might find a blue (5) rupees. It may be small, but you can do it infinitely.