The safest (and easiest way) is to provide a path relative to the root folder. That way, the same path works no matter where it's placed in the site. If you want a link to the jQeury file on each page, for example, this is the way to go.
So let's say you have a folder in your site's root folder (where your home page is) called /scripts/, and in there is your jQuery library script, jquery.min.js or whatever. You can link to that file from anywhere in your site with:
The only caveat is that these root relative links (with the slash at the front) don't work on your desktop version, unless you have a virtual server environment set up.