Easy Rupees
Takuri
This is that really annoying bird that flies at you and steals your stuff (remember, 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. Pull out your bow and shoot Takuri till he dies (I like to use Light Arrows). 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.
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.
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.