The content canonical plugin resolves the issue with multiply URLs of single article. So if you have component/content/article/32-something.html and something.html, now both will be indexed from one URL (something.html).
It fixes the major part of the bugs in the Joomla! 3 core canonical routing.
The exact structure of the canonical URL, depends on your menu structure.
Since version 3, it fixes the homepage canonical, article canonical, category canonical, redirects tag to a single page, removes all Joomla! canonical links (these are broken). It overal fixes all major bugs with Joomla! canonicals.
In order the tags to work correctly, you must have at least one menu item linking to a tag.
The plugin is updated to work with latest version of Joomla!
v3.1 - 31.12.2013
[^] Fixed bug for subdomains and sites in folders
v3.0 - 02.11.2013
[^] The whole plugin has be re-written to work with Joomla! 3.0
[+] Fix the home page routing
[+] Redirect all tags duplicated pages to a single one.
[+] Fix category canonical
[+] Remove the buggy Joomla! canonical link