A question on this one, but first I'll answer Sean's question with link to a video
from Matt Cutts. Or if you want he also has shorter one
that's more on point to your question. Matt says you can
add rel="canonical" to each page, but he doesn't recommend it. I concur with his idea that it's better to fix the actual cause of the problem than try to patch it up with what is effectively a bandaid. Matt makes a good case in the videos about some situations could go very badly wrong. And how someone could easily harm their site's ranking with a canonical tag that caused confusion.
Now, on to my question.
Since Matt and others have referred to this as a mini 301, and since they're basically replacing one page uri with another, is it safe to assume PageRank/Link Pop will flow through to the destination page? I think it probably does given the hints I've read and heard from those who should be in the know.
The reason I ask is simply that rel="canonical" could be a very easy way to deal with affiliate links/traffic where the url contains the affiliates code. You could even let it carry on through each page of the site visit if you wanted. Or only have the rel="canonical" get slapped in the page when the affiliate code was in the query string.
Has anybody gotten a solid answer on the PageRank/Link Pop pass through with rel="canonical" yet?
FWIW, the best I've gotten so far is: It should. But it's not guaranteed to pass through. Which isn't quite good enough to for me to start recommending it as a valid option.