The rel="canonical" attribute was recently introduced  by Google  (and it was also adopted by other search engines)  to indicate the preferred link from a set of different URLs that generates the same content :

http://www.mydomain.com/shoes/red.html?gclid=XY
http://www.mydomain.com/shoes/index.php?product_id=10&highlight=shoes+red&cat_id=7&sessionid=21

 

Could rel="canonical" be  used for Joomla! websites?

Yes, actually it is recommended because Joomla! or 3rd party extensions could generate  different links to display the same content like in the above example.

Each URL should display unique content and this unique content should only be accessed trough a single URL.

• Read More...

Let's say you are quering Google for "red shoes"...

...and you find the following links in Google index:

• http://www.mywebsite.com/index.php?option=com_content&task=view&id=5&Itemid=1

• http://www.competitor-website.com/shoes/red

which link has better chances to actually being clicked?

Why enable SEF from Joomla! ?

1. Search engines: Pages with dynamic URLs generated by Joomla! aren't optimized for search engines and won't rank higher.
   That's why it is necessary to enable SEF from Joomla! to rewrite the default Joomla! URLs .


2. Security reasons: In search of vulnerabilities, someone could google for Joomla! specific url "index.php?option=com_content...." and find your website listed in search engine results page. 
   They will try to enter in the backend administrator using different techniques like brute force attempts and SQL-injections.

How to enable SEF from Joomla! ?

1. In the backend administrator panel head to "Site" -> "Global Configuration"
2. In the right panel enable "Search Engine Friendly URLs" from "SEO Settings".