Everyone is aware that duplicate url/content causes a negative effect on search engine, worry no more because Google, Yahoo, and Microsoft already made an action to solve the issues. The three search engine company announced the support for the new link tag to clean up duplicate urls on sites that produces duplicate content.
Here an example on how canonical link tag works. If you have a blog post URL: http://www.eligio.org/kakashi-is-dead-naruto-shippuuden-mad-spoiler.html and you have a lot of comment on that topic, this produces duplicate url/content. See URL with comment http://www.eligio.org/kakashi-is-dead-naruto-shippuuden-mad-spoiler.html/comment-page-2#comments . Both URL produces duplicate content, so in order to prevent this, We use the new implemented link tag, this will be added under the HEAD tag.
Example Canonical Link Tag
<link rel="canonical" href="http://www.eligio.org/kakashi-is-dead-naruto-shippuuden-mad-spoiler.html"/>
The canonical link tag tell the search engine that the preferred location is specified in the link tag. This is the same function as when using 301/permanent redirect.
If you are using wordpress/drupal, Joost de Valk has already made canonical plug-in for WordPress and Drupal module.
To learn more about canonical link element you can visit Matts Cutts Blog.
