If you run into the JavaScript exception while attempting to add AJAX.net animations to your controls there is a setting in your web.config that you need to update. Open your web.config and locate the tag

<xhtmlConformance mode="Legacy"/> and replace with <xhtmlConformance mode="Transitional"/>.

One odd thing you need to keep in mind when using AJAX.net and the AjaxControlToolkit is that when the UpdatePanel is used to do an asynchronous call back to the server the entire page state is sent back to the server and the entire page is reprocessed. This means that everything in your Page_Load and other initialization methods will be called again.