Basic structure related to plugin and application layout. Originally this was devised based on how the jQuery team recommend you create plugins. I simply modified it to encompass application related JS. Generally we place this either directly at the bottom, or within a JS file referenced at the bottom of the page.

plugin-app-structure.js

(function(window,$,undefined){
    
    if(typeof $ == 'boolean' && $ == true)
    {
        return;
    }
    
    //-- basic settings using descriptive prefixes
    var _settings =
    {
        url_someurl     : 'someurl.file',
        obj_somedesc    : $('#someselector'),
        link_somelink   : $('a#somelinkselector'),
        class_someclass : 'someclass'
    };
    
    //-- internal
    var _data =
    {
        mydata : null
    };
    
    $(document).ready(function()
    {
        //-- do something
        _somefunction();
    });
    
    
    function _somefunction()
    {
        //-- local references
        var url_someurl     = _settings.url_someurl,
            obj_somedesc    = _settings.obj_somedesc,
            link_somelink   = _settings.link_somelink,
            class_someclass = _settings.class_someclass;
            
        //-- doing stuff
    }
    
})(this,(typeof jQuery == 'undefined' || jQuery));