Going from the first few years, colours to allegiance would be:

Autobots:
-Red (big one there)
-Yellow
-Green
-Light blue

Decepticons:
-Black
-Grey
-Purple
-Dark/Navy Blue
-White

There are a few exceptions, but I seem to like the little more diversity the Decepticons can have. They seem to be able to have a lot more colours, whereas the Autobots kind of have a boundary.