I had a hard time finding any indication in Google searches for this - so I just thought I'd document it here. If I ever get anything with Mootools to work again, I'll post an update. So far it looks like DNN will play nice with Prototype so that may be the route to go if you want to use one of these ever popular Javascript frameworks with DNN.
EDIT: Per R Doom in the comments I checked out what I could do with JQuery. It works well enough with DNN but you've got to over ride $ functions using calling the neato noConflict ():
<html>
<head>
<script src="jquery.js"></script>
<script>
jQuery.noConflict();
// Use jQuery via jQuery(...)
jQuery(document).ready(function(){
jQuery("div").hide();
});
</script>
</head>
<body></body>
</html>
More info here about noConflict.