You can add this in your css file:
[data-role=page]{height: 100% !important; position:relative !important;}
[data-role=footer]{bottom:0; position:absolute !important; top: auto !important; width:100%;}
So the page data-role now have 100% height, and footer is in absolute position.
Also Yappo have wrote an excellent plugin that you can find here:
jQuery Mobile in a iScroll plugin
http://yappo.github.com/projects/jquery.mobile.iscroll/livedemo.html
hope you found the answer!
An answer update
You can now use the data-position="fixed" attribute to keep your footer element on the bottom.
Docs and demos: http://view.jquerymobile.com/master/demos/toolbar-fixed/