Boilerplate for JavaScript module pattern http://addyosmani.com/resources/essentialjsdesignpatterns/book/#modulepatternjavascript

jquery.site.js

// One global variable for all your JavaScript
var MY_SITE = window.MY_SITE || {};

// Requires jQuery
// Global jQuery object is aliased to avoid polluting global namespace with "$"
MY_SITE = (function ($) {

    'use strict';

    var private_function;

    // Private function
    // Can only be called by public functions below because of closure

    private_function = function () {
        return;
    };

    return {

        // Public function
        // Can be called "outside" of this closure on an individual basis
        // e.g. MY_SITE.public_function()
        // Or can be bundled in single function meant specifically for page load
        // e.g. MY_SITE.init()

        public_function: function () {
            private_function();
            return;
        },

        // Open a new window for external URLs
        openNewWindow: function () {
            $('.js-external, a[rel="external"], a[href*=".pdf"]').click(function (event) {
                window.open($(this).attr('href'));
                event.preventDefault();
            });
        },

        // Initialize function collects all functions meant for every page load
        init: function () {
            var self = this;
            self.openNewWindow();
        }

    };

}(jQuery));

// Call initialize function ONCE
// There is NO NEED to have a dozen disorganized document.ready() functions
jQuery(function () {
    'use strict';
    MY_SITE.init();
});