Mohammed the Persian

I may be a bit late to this party but here goes

Black was traditionally used by the Prophet's army, and later on by the Abbasids.

White was traditionally used by the Ummayeds.

Green was used by the Shia Fatamids (Green being the colour of Ahlulbayt, the Prophet's household)

And if you're wondering about the Kharijites, they used red

Salah

During the lifetime of the Prophet many newly-Muslim tribes continued to carry their traditional banners, I don't know how long this custom continued however.

AndreasK

And which colour of flag did the Caliphate / Emirate of Cordoba use?