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" />
What is the _references.js file used for in a new ASP.NET MVC 4 project?