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1. Links from FFA pages or other pages with PR=0
2. Links with 3 or more variables.
3. Links with "ID=" as one of the variables (I believe).
4. Links to duplicate pages that get may filtered.
4 is the killer for affiliate links. If Google matches the page linked to by the affiliate with one that already exists in the index then there's a good chance that the page will be filtered out as a duplicate page and the pagerank won't get counted.
If you think about it, Google has no option really. Otherwise you could just create thousands of internal links to your home page of the form "www.widgets.com/index.php?var1=a&var2=b" and expect google to treat them all as separate pages and give you a huge PR boost. Believe me, this wouldn't work if you tried it.
If I was you I wouldn't worry about the PR of affiliate links. Use affiliates as a way to bring more customers to your site and if you do get a PR boost count yourself lucky.
Mike
4 is the killer for affiliate links.
And so is 3. The user tracker code is seen by Google as a new page. mydomain.com/mysite.htm?usertracker will receive the PR. Not mydomain.com/mysite.htm
And third party affiliate programs. All affiliates linking to myaffiliate.com are not helping mydomain.com at all.
After reading the advice above, i've now got my referal links to 301 and am hopefully looking for a change in a few months.
Thanks for the heads up on the 301 redirect...
Regarding 301 VS 302, you'll have to decide, I don't recommend one over the other as I haven't studied that situation closely yet.
SN
3. Links with "ID=" as one of the variables (I believe).
4. Links to duplicate pages that get may filtered.
Strange. Last week I I realized that by coincidence I had raised the PR of my affiliate page (external to my site, the link containing "?id=string") to a PR3 just by placing banners. Never intended to do this :)
Giving your affiliate page decent PR with some good anchor text from your content pages might be a good strategy in some cases.