Jupiter appears to be many colours because is has bands of clouds in its atmosphere. We sometimes see through the clouds to different layers beneath – the colours of the layers depend on which chemicals they are made from.
Some of the colours are caused by amonia ice, amonia is that really smelly stuff you get in some cleaning fluids.
Other bands of colour are caused by organic molecules, but we’re not sure in detail quite what they are all made up of… we need another Jupiter mission, of which we happen to have one! http://en.wikipedia.org/wiki/Jupiter_Icy_Moon_Explorer
although its going to spend most of its time looking at Jupiters moons
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