The Paint Brush is used to color Pneumatic and Redstone Tubes. It is designed primarily for sorting (items may be assigned colors by Filters or Sorting Machines, for example), but the colors can also serve to prevent tubes from connecting to each other, similar to the Painter from IC2. Tubes that are painted will accept only items that have been assigned the same color.
A Paint Can is required to refill the Paint Brush when it runs out of Paint.