Points
Colored cups result in more points if you drop balls in them, and the balls will change color. Then, drop those colored balls in clear cups for more points.
The more balls and cups you have available, the easier it will be to keep adding points. Only give up cups when necessary.
Various strategies
Do not place too many balls in the same cup or your drops will get too difficult.
When a large number of cups begin appearing in later levels, let some pass so the screen does not get too cluttered.