I'm rewriting my cms to better handle multiple cross-linked domains. Though I can make 99% of nav and file calls within the domain or even between domains use proper urls, a few calls between domains hosted on the same server may be linked through the server's root domain. The cms can automatically generate a page's absolute canonical url when it's processed, so it'd be a no-brainer to put the rel=canonical tag in the template as a belt & braces fix. I'll do that unless someone here has had problems caused by canonicals.
I'd say do it. We had a big problem this year that would have been significantly reduced by having this (couple of million extra urls indexed across 3 domains on a common platform - big panda hit)
If you can code it such that the canonical tag is only deployed when needed, and not pumped out across every page regardless, I would do that.
I think the one thing to watch for is the same gotcha as for sitemaps: if you have problems with your basic setup that causes Google to assign a non-canonical URL to a page (or in the case of sitemaps, to crawl a page it wouldn't otherwise discover), you are losing a possible diagnostic signal about your site because you can no longer see which URLs Google would consider to be the strongest.
I'd probably insert the tag into the template. So not saying it's a bad idea, just that there is a small secondary consideration there.
Ideal: tweak the site until Google gets it righ
Practical: add the rel tag
>only deployed when needed
>ideal
Right. Since my cms writes static clientside and then overwrites the server, I'm going to be stuck with all-or-none unless I can come up with (yet another, hhh) brilliant coding solution. Either that or manually assign a different template to any page that is linked to --which seems too likely to be forgotten. The sites are live and have a few pages indexed so, given that no one here has thrown themselves bodily across the path of this idea, I stick them in the template and see what happens.
I've had to do this (I *hate* having to resort to stuff like canonical) on one site and have seen nothing to indicate it's caused any problems. It didn't magically increase rankings where there was a problem either, but at least its showing 'good intent' on some issues which I;m struggling to solve properly, if G ever decided to get stroppy.