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In your case you have to put canonical tag on "affilaite landing page". For Example :

Landing Page : www.example.com

Landing Page for Affiliate : www.example.com/?aff_id=10

Both the pages has the same content so to come out of this you have to put below tag in affiliate landing page

rel="canonical" href="www.example.com" />

Other Solution: You can block these affiliate pages in robots.txt or by putting noindex,nofollow meta in "landing page for affiliate.

Hi,

I have good links for you. Few days ago John Doherty has written two nice blog post on it.

http://www.seomoz.org/blog/smarter-internal-linking-whiteboard-friday

http://www.seomoz.org/blog/internal-linking-strategies-for-2012-and-beyond

Hope below links help...

There are various plugin available in Joomla for URL Canonicalization. You can try below plugin :

http://extensions.joomla.org/extensions/site-management/seo-a-metadata/url-canonicalization-/16432

Can't you show message "Product is out of stock for now" message. And show related product below with "You might be interested in below product"  message.