Here is a video about the beginnings of our theories and experiential understanding of nut materials. As we said in the Rules of Tone segment on our Phase III Tuners: every part of a guitar has an effect on its overall tone. The nut is no exception. Some things are pretty obvious...the nut should not "grab" the strings, for example. What may not seem so obvious, is the importance and impact the selection of nut material can have. The nut material should always add to the resonance of the guitar. To exaggerate it and boil it down to the bone, almost anyone will admit that a guitar with a silicone rubber nut will sound different than a guitar with a steel nut. It is definitely an important piece of the puzzle.
For more on the Rules of Tone, visit http://www.prsguitars.com/index.php/blog/category/rules_of_tone