I like it when someone at the Factory chimes in with some insight like David Conant did at the AUGI forums the other day. Regarding a members confusion about the new material concepts added to Revit 2012 he wrote:
Think of the Material as a container. It contains sets of information that represent different aspects of materiality: Appearance (what it looks like in a rendering), Structure (how strong it is), Graphics (what it looks like in a non rendered view), and general information about the material. In some cases (appearance and structure) the information can be provided to the material by linking to a seperately defined property set (by Property Set), or can be input directly into the material (Independent). This allows several materials to share a single set of properties and changes to that property set to propagate to all those materials.
Imagine you are working with several materials of different types that are all covered with the same finish, green paint for example. In that case you would create as many Materials as needed and assign the same green paint appearance property set to each. To change the paint tint on all, change the definition of the appearance property set. The appearance of all those materials will change together.
Conversely, you might have four kinds of concrete with the same strength but different appearances. In that case you would create the four concrete materials linked to the same Structure property set, but with different appearances.
If you need to tweak the appearance of an individual material without changing any others, set its appearance property to Independent. Your changes will then be confined to that material only.