Why do the atoms in molecular models have the colors they have?
There's an interesting article here - Illustrating Atoms and Molecules - that discusses atom colors:


  In 1865, the chemist August Hoffman gave a Friday Evening Discourse at London’s Royal Institution on the “Combining Power of Atoms.” In order to demonstrate chemical bonding of atoms, he drilled holes in croquet balls and connected them with metal pipes (Figure 2). His choices were limited by the available colors of croquet balls and he relied on many of the same color conventions that had been adopted centuries earlier


These colors are listed as :


  
  Carbon is colored black because it’s the color of charcoal.
  Oxygen is red because it’s necessary for combustion.
  Nitrogen is blue because it’s the most abundant element in the
  Earth’s atmosphere and the sky appears blue.
  Hydrogen is white because it forms a colorless gas.
  Chlorine is green because it forms a greenish gas.
  Sulfur is yellow because that’s its color in mineral form.
  Phosphorus is orange because it glows orange in a flame.
  Iron is reddish brown because it rusts.
  


Which is interesting, but I've no idea where this list comes from...