When Google announced support for the canonical tag just about a year ago, webmasters were excited for the possibilities of a serving a 301 redirect to spiders but not users. But when should you not use it?
A Google Webmaster Help thread has Google's JohnMu explaining some situations as to when you should or should not use it.
In summary, think of the canonical tag as a real 301 redirect for spiders. If a spider is redirected away from new content, then that is an issue. When it comes to paginating content, such as product category pages or article archives, you really need to give a way for search engines to find that content. If you set the canonical tag to redirect spiders from page 2, 3, 4, etc of your product category pages to page one, then the spiders might never be able to index the products on page 2, 3, and 4.
John explained this well, saying:
This is something to keep in mind when building out the canonical tag within your content management system.
Forum discussion at Google Webmaster Help.