I have a little over 50 domains parked on top of a main domain, then I use PHP to show content based on the domain. So in the end, whatever.com is identical to example.com/whatever, whatever1.com is identical to example.com/whatever1, and so on.

The question is, should I (and is it allowed to) set the <link rel="canonical" href="..."> on example.com/whatever to whatever.com? Even though the viewer is actually on example.com, I'm thinking that the search engines should only be looking at whatever.com. And since the search engines probably see them as duplicate pages (which i understand can result in a penalty), I would want any search engine preference to go to whatever.com.

Or should I do it the other way around, setting the canonical for all of the whatever[0-9].com sites to example.com/whatever[0-9], in the thought that 50+ domains that are linked back to one will give all of their search engine placement power to it, resulting in a greater single domain than the 50 domains would have separately?

What do you guys think?