[eluser]mmarcus44[/eluser]
jQuery is javascript, which is a client side/public file. The best thing to do is put this in the same folder or subfolder as your images and css.
Anywhere outside the application directory is good.
If you have disabled the index file from appearing with apache rewrite, make sure to update your .htaccess file too.
The reason you should update this file is if you decide to create a new directory for js files only.
BTW jQuery rocks!