To control the colors of each of the 9 RGB LED's individually is the same as controlling 27 LED's.
Normally this is done using PWM, but Arduino does not have enough PWM pins to do that.
One solution would be to use a PWM driver IC like the TLC5940. (You would need two of thwm).
Here's a link to one place to get it: http://www.sparkfun.com/products/10136.