While Radhil gave a great answer, there are great a many more references to a what a wise man's fear is.
Quite obviously, there is a recurring red thread within the story of Kvothe. Lots of this is based on the titles; "The Name of the Wind", "A Wise Man's Fear" and presumably "Doors of Stone".
All of them basically have to do with the origin story of the world as they know it, main subjects of the story in general and the metastory.
Why is there a mortal realm and a Fae realm? There are certain universal truths true for both worlds, such as the undisputed power of names. Kvothe was able to, if he so willed it, destroy Felurian after learning her name. Nevertheless, most mortals would perish under the power of Felurian. It is safe to assume that there are a great many of the Fae with immense powers, as long as these remain in the Fae realm.
"A wise man views a moonless night with fear", as chapter 102 was concluded by Felurian. Why? Because, "each step you take might you in the dark moon's wake, and pull you all unwitting into fae, where you will have no choice but stay. And on such unfamiliar ground, how can a mortal help but drown?". Obviously, this is important information. Not only for understanding the universe, but this might explain the sudden disappearance of the Outlaw's leader a few nights before this happened. Despite having an experienced tracker, there were no signs of any trail.
Felurian refuses vehemently to any information giving on the Chandrian. This implies a strong link or influence of the Chandrian on the Fae.
Also, the importance of this link of the wise man's fear is emphasized in the beginning of the book by Elodin at Kvothe's tuition at page 88: "You want me to ask him questions only a namer can answer? Fine. Where does the moon go when it is no longer in our sky?"
It is linked with the title "Doors of Stone", at page 670 Felurian describes the namer responsible for the divergence between the Fae and mortal realms "I will not speak of that one, though he is shut beyond the doors of stone."
I'll write a more coherent segment on this later, but if you are frustrated with the title of the book, there are actually loads of potential references and meanings one may extract.