Are you asking about in the program, or in reality?
In reality, yes - composition and temperature affect the colours. See
http://en.wikipedia.org/wiki/Sudarsky_e ... sification for info.
Banding will be affected by things like atmospheric haze (high altitude haze will hide the bands, as in the case of Uranus IIRC), and hot jupiters in torch orbits will have much more turbulent patterns on them due to winds caused by the obscenely high temperatures of their day side.