The most important rule when aiming for a high score is to think ahead: each group you remove will form and destroy other groups.

Remove higher groups first, unless removing another group will make it larger. Vertically aligned objects can't be misaligned, but horizontal arrangements can.

Since the score increases quadratically, big groups of objects are always better. For example, the points difference between a six object group and a seven object group is nine points. In a situation where you have a choice between merging two groups of two into four or just adding one more to the group of six then you should add the single object. Even though the groups of two you are left with score no points, the bigger group scores more overall.

Don't forget the thousand point bonus for clearing all the balls. To get 1000 points from a single group you need 34 objects. You are very unlikely to be in a position where you have to sacrifice a group that large to clear the board.