The Commonwealth Railways had two main colours for there wagons, a dark red and a dark brown. I do not know the significance of the colours although much of the narrow gauge was dark red and much of the standard gauge was dark brown. With many wagons changing gauges and being reclassified, this may have given rise to the variations in train colours that we have seen and that are recorded in many photographs.
Some wagons painted in CR wagon red had a black chassis and bogies, so for a correct paint job on your model you will need to check photos of the wagon you are modelling. For the wagon red use Floquil Boxcar Red.
Wagons painted in CR wagon brown were painted wagon brown all over. For wagon brown use Floquil Tuscan Red with 20% Reefer Orange or use Floquil SO Freight Car Brown.
Passenger stock on the Commonwealth Railways was painted in several different colours at different stages. Some of the passenger stock was painted cream and chocolate while others were painted a bright red. For the Cream and Chocolate use Humbrol 7 and Floquil xxxx. For the bright red use Humbrol 19 with a few drops of Humbrol 25 (blue).