I activated Cart66 Lite and immediately all my animations and fades and whatnot stopped working. A little bit of poking around revealed lines like this in most of the .js files:
var $j = jQuery.noConflict();
Basically, this kills all of my "normal" jQuery code (i.e., "$(".thing").val("hello");".
Has anyone else had to deal with this? Is there a way around it without either modifying the plugin's code or changing every jQuery call in my theme?