From StrategyWiki, the free strategy guide and walkthrough wiki

These were the second most valuable rupee in Twilight Princess next to the silver rupee. Now they can be found in most stages for a maximum of 1000 points! These rupees are found in pots, barrels and sometimes skulls, so start shooting. Also, when a rupee appears it will begin floating up and down. The longer the rupee stays afloat, the fewer the points it will give you until it vanishes.

Stage	Rupees	Location
1-1	1	Pot on right side of Mayors house.
1-2	2	Group of skulls to right once you start. Pot off in the distance on stone pedestal.
1-3	2	Pot on left once you start. Behind tent with explosive barrel.
2-1	3	One in each area behind Gorons. Just look for the pots.
2-2	3	Two found in the first four pots on the river. Third is in top pot of a group of five with a red pot in the middle.
2-3	1	In the barrel in the center of the stage.
3-1	1	Pot on right of Malo's Shop.
3-2	1	Barrel down in town center to the left.
3-3	1	Found in skull on fence post.
4-1	1	In second area in center of stage.
4-2
4-3
5-1	1	Second area in entryway.
5-2
5-3
6-1
6-2
6-3
7-1	1	Second area found in skull along right wall.
7-2
7-3
8-1
8-2	1	Found in icicle stalagmite in front of cave.
8-3	1	Pot alongside wall.
F-1	1	Pot inside of barn.
F-2
F-3