There are many extensions that add canonical URLs to product and category pages, but what’s up with CMS pages? There is no need to access your FTP to edit files. To add a canonical URL to a CMS page, simply navigate to the CMS page in the admin panel and then add the following to the Layout Update XML text area under the Design tab:
<reference name="head"> <action method="addLinkRel"><rel>canonical</rel><href>http://www.yoururl.com/goes/here</href></action> </reference>
You’ll have to add this to every page individually, but you should be entering meta data anyway.
Source : http://www.magentocommerce.com/wiki