Reference Guides
A package reference guide is one document that begins with a package description and contains all the contents of the .Rd help .Rd for packages. Typically, this means that it has help files for functions in the package, any documented datasets, and documentation at the package level (if included). It is automatically generated from .Rd sources.
Each package has a manual. Even a package without exported functions and documentation should still have a manual (when creating it) consisting of text from a description file.
vignettes
Vignettes are free-form documents. Typically, package authors use them to demonstrate the use of their package. They are optional, some packages have several (since I write this dplyr has 8 vignettes ), and many packages do not.
As mentioned in the comments, the R Extensions Manual is the ultimate source of everything related to the package. Here is Josh’s link to the Vignettes section and 2.15 Processing Documentation Files describes how the reference guides are created.