Usually, every time you create a new Web API project you:
Web.config file(s) to remove the elements that point to the assemblies which have been removed.Use the Empty ASP.NET Web API Project Template. The Visual Studio extension can be downloaded from here.
It will add a new project template Empty Web API which includes the following:
A favicon.ico file is included because the browser requests it so it’s better not to respond with a 404 Not Found.
Update (2013/10/06):
You may install Newtonsoft.Json through NuGet:
PM> Install-Package Newtonsoft.Json
Depending on the configuration, the Newtonsoft.Json package is included because it is can be lazy loaded inside the System.Net.Http.Formatting.JsonMediaTypeFormatter type.