To add a custom canonical tag to your CMS page you can achieve this by using the custom layout update XML section within the Magento admin. This can be exceptionally handy if you utilise a CMS page for your homepage where multiple versions can be accessed.

<reference name="head">
<action method="addLinkRel">
<rel>canonical</rel>
<href>http://www.domain.com/url/</href>
</action>
</reference>