This probably isn't the most efficient way of approaching Canonical URLs, however, it works, and sometimes that's good enough. Feel to offer better solutions.

Pages

/templates/pages/attributes/seo.html

<link rel="canonical" href="<perch:pages id="url" type="hidden" />">

Collections

/templates/content/projects/seo.html

<link rel="canonical" href="<perch:content id="domain" type="hidden">/projects/<perch:content id="slug">">

Note Collection name is inputted manually.

Blog

/blog/meta_head.html

<link rel="canonical" href="<perch:blog id="domain" type="hidden"><perch:blog id="postURL" type="hidden">">