The new unified material library in Inventor 2013 and other Autodesk products allows to manage both visual (color, appearance, transparency...) and physical material properties in a single place.
You can extend the predefined material library with your own materials, create new libraries, or change properties of the existing materials.
The material editor can be invoked through the ribbon Tools > Material and appearance > Material. Double-click on a material to launch the editor dialog, where you can adjust the material properties and assets - color hue, reflections, transparency, but also thermal conductance, Young modulus, density, yield strength, etc. The editor window is split by aspect to "Appearance" and "Physical" tabs: