Click on a contiguous blob of balls of the same color,and they will light up. Click again, and they all go away. When they go away, balls above them will drop down in accordance with physics. Also, if a column becomes completely empty, the columns to the right of it will slide to the left in order to close the gap. This has nothing to do with physics, but makes it much easier to clear the playing field.
To qualify as contiguous, balls must be above, below, to the left or right of each other. That is, diagonals don't count.
The game tells you your current score at the right of the applet, as well as the current numbers of red, blue, and green balls. This information is provided to help you plan your strategy. Also on the right of the applet are buttons to start a new game and to restart the current game (if you made a mistake, want to compare different strategies while keeping other variables constant, or want to play against a friend). Refreshing the webpage will also work to start a new game, but I like my buttons.
When you vaporize a group of balls, you get points equal to (n-2) squared, where n is the number of balls in the contiguous blob. Thus, a group of two balls would give no points when destroyed, a group of three would give 1, four would give 4, five would give 9, and so forth. You aren't allowed to click on just one ball.
If you manage to get rid of all the balls on the game board, you get a bonus of 1000 points.
There is no way to definitively "win" or "lose" SameGame. You can just get a higher score or a lower score. Currently I don't have the skill or inclination to build a highscore tracking device into my applet, so you'll have to remember how well you've done yourself. My high score is 5860, but that was on an especially copacetic game.