As with Blender Internal materials, Cycles materials can (and should) be organized to optimize not only your workflow but also Blender memory management.

Material nodes can easily grow quite complex in Cycles so it's sometimes a good idea to split and label the different parts of a shader's network, just to make the meaning of the different sections more clear (even to yourself; maybe at a certain point of your workflow, you forget how exactly you organized the 120 nodes of material you made a couple of months before working). Moreover, organized materials can be easily reused in other files, projects, or as parts of bigger and different materials.

The organization of the materials basically is made by grouping them and/or giving them proper names and defined locations, so as to be easily found on the hard disk.