If we're talking about a complete app, then it depends on what you're planning to use on the server side. Take whatever that is, and include Backbone (and appropriate dependencies) in your HTML. You're off to the races.
Saying what the best "skeleton" is would be like saying that there's a particular skeleton app you should always use when starting a project that involves jQuery.
Saying what the best "skeleton" is would be like saying that there's a particular skeleton app you should always use when starting a project that involves jQuery.