//wait for document.ready to fire

$(function () {



    //then load the JavaScript file

    $.getScript('script.js');

});

http://api.jquery.com/jquery.getscript

//create a callback function

function myCallback () {





    //create a script element and set it's type and async attributes

    var script = document.createElement('script'); script.type = 'text/javascript'; script.async = true;



    //set the source of the script element

    script.src = 'script.js';





    //add the script element to the DOM

    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(script, s);



}



//add event listener for the deviceready function to run our callback function

document.addEventListener(deviceready, myCallback, false);

http://docs.phonegap.com/en/1.4.1/phonegap_events_events.md.html#deviceready

This second code snippet is a slightly modified version of the Google Analytic code, used to add a script to the DOM asynchronously.

UPDATE

You can also set the defer attribute of a <script> tag to true and it won't be executed until after the DOM has been prepared. See some documentation here: https://developer.mozilla.org/en-US/docs/HTML/Element/Script