What is the _references.js used for?
In VS 11, Visual Studio will give you intellisense from all files that have references in the “_references.js” file.
MSDN documentation: JavaScript IntelliSense
In brief, _references.js stores the list of JS files paths, for which you want the Visual Studio to gather and build the intelisense (aka "code complete"). The VS project adds there some common JS libraries like jQuery to build the intellisense for it. You can add a reference to your custom JS file in form like this:
/// <reference path="MyScriptFile.js" />