The Normal profile uses the following color scheme: XYZ -> RGB, that is, colors Red, Green, Blue correspond to axes X, Y, Z. Handles that are located on the axes or that are tied to the axes by transformation (rotation around the axis) have the color matching that specific axis.
Shades of Red, Green, Blue are used either for auxiliary highlight geometry (which appears when the mouse cursor hovers over a handle):
Using Using light red color for highlight geometry
Or to differentiate an 'accurate' (i.e. with snap) handle from non-accurate:
Using light blue color (on the right) to mark imprecise rotation
The Yellow, Magenta and Cyan colors are used for the handles that work in XY, XZ and YZ planes, respectively.
Another possibility for planes was is to paint the handles using the colors of corresponding axes, for example, paint one half of the handle red, the other - green. 
But as the handles themselves are small, this type of coloring is often not visible enough.
Light Gray is used for Anchor
Colors used in the Normal profile.
First versions of Conceptual Selector used materials, but that approach presented a number of shortcomings. Selector materials need to be included in the database, and they need to be on the user's machine, which is not always possible. User might change or delete those materials. At the moment, Conceptual Selector uses only colors (pen colors) and does not use materials. Nevertheless, users can use materials, with textures as well. Naturally, it should be noted that not all effects of materials are available in draft mode.
In practice, it is impossible to pick a color scheme that would make each and every user happy. Conceptual Selector technology has adjustable color scheme. Users can edit colors, transparency and materials in any TCW profile.