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Speaking from both a usability standpoint, as well as a PR standpoint, I think it would make little or no difference either way.
However, you may have better luck getting backlins when using third-level domains, because you might get others' individual sites to link to multiple portions of your site since they are on different domains. But I believe this is more of a psychological characteristic than a technical one.
Do a WebmasterWorld site search for canonicals, subdomains and navigation structures. You should also look through the various posts of the fellow member paynet - she's got great insights and experiences with the usage of canonicals. She moderates the Link Development Forum [webmasterworld.com].
From my experience: i use canonicals for the main themes of a large specialized directory. 1 main site - 3 canonicals. Since my site is really well themed and organized it works great. There are huge benefits allthough some risks. It's all about themeing and you should definitely check the posts here at WebmasterWorld related to canonicals.