How to get the active #comment-cid when a comment permalink is clicked?
Try to add a custom javascript file to in theme.info file

 jQuery(document).ready(function() {
    //get the current path
    var pathname = window.location.hash;
    jQuery(pathname).next().addClass('active-comment');
    //here add your custom animation
    jQuery('.active-comment').fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn().fadeOut().fadeIn();

});


here is a plugin to animate the background color of the wrapper :here

Hope this will Help You