one of the way i reference libraries in non-web projects (websites) is by creating a text file with .dll.refresh as the extension.
lets say i want to add Elmah.dll as a reference in website.
so in my Website's Bin folder (Website\Bin) i create a file called Elmah.dll.refresh file which is a plain text file.
inside that text file (Elmah.dll.refresh) add the following line.
when msbuild (or visual studio) compiles the website it auto copies the Elmah.dll (class library), Elmah.pdb(debug information) and Elmah.xml (xml documentation). if it doesnot exist it skips.
might be nupack can have this feature, either to set as a reference if its a web app, or create a .dll.refresh file and copy it to the bin folder if it is a website.
Advantage to it is that the .dll.refresh files can be in source control too. (i usually ignore all the files in Website\Bin folder except the .dll.refresh files).