Making themes to be prefect was never ending story. When we try to make a new breakthrough with new stuff into our themes then there will be more and more customization.
 jQuery is one of wordpress compatibility besides prototype library. For an example I took jQuery lightbox plugin from pedrolamas. This plugin make your thumbnail more pretty.
The major purpose Customizing themes with jQuery is how to make the reader more comfortable and enjoy to read the information.
Another example of using jQuery is Events Calendar. You can manage the event calendar and shows up into your blog/site. Or maybe you need a custom comment with ajax like WP Wall which is put your comment at the sidebar and update directly without reloading the page.
WordPress is not ordinary blog CMS but it could be more complicated even you could build a portal from this WordPress and of course using the match plugin or create it would more powerful.
Still confusing with jQuery, use the plugin that already has jQuery and customize your themes now, have a nice practices.
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