dr_pete - 1:24 pm on May 18, 2011 (gmt 0)
I'm running an experiment to try to exploit Rel-canonical in the <body>, and, consistent with Matt's statement, it doesn't seem to work (even on the same domain). The comment about a a bad <head> (unclosed or doubling-up) may be worth testing, but I think Google is pretty good about ignoring secondary <head> sections.
On the other hand, every experience I've had with Rel-canonical suggest that it's VERY powerful and much more than just a suggestion. Even cross-domain canonicals seem to be working much more often than I would've originally expected.