You need to give the full path to your theme files. To get the URL of your theme, use the WordPress function bloginfo( 'template_directory' ); so at a minimum you would need:
<script src="https://wordpress.stackexchange.com/questions/18828/<?php bloginfo("template_directory' ) ?>/jquery.js" type="text/javascript"></script>
However, scripts / styles should really be “enqueued” using wp_enqueue_script(); (see http://codex.wordpress.org/Function_Reference/wp_enqueue_script)
I would recommend taking a look at some other themes to see how they include thetheme files like this. Also the Codex page on Theme Development is a good place to start: http://codex.wordpress.org/Theme_Development
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