Great article and introduction into this important subject, but one remark, the example you give will not work for several reasons:
The nofollow tag needs to come after the link, as it is a link attribute and if you want to make site.com a clickable link you need to format it differently, like this:
As the comment form, most likely will convert my example into a link, just replace () with <> to get the proper code:
(a href="
http://www.site.com/" rel="nofollow")site.com(/a)
<a href="
http://www.site.com/" rel="nofollow">site.com</a>
Hope that helps somebody, SY