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I just read through Lawrence Deon's inciteful look at Google's recent Patent filing, and what struck my as most interesting was the part about potentially punishing sites for having "too many" affilaite links and also potentially punishing sites that link to pages with too many affilaite links.
Here is the section of his post I found interesting:
According to their patent filing Google records and scores the following web page changes to determine freshness.

• The frequency of all web page changes
• The actual amount of the change itself… whether it is a substantial change redundant or superfluous
• Changes in keyword distribution or density
• The actual number of new web pages that link to a web page
• The change or update of anchor text (the text that is used to link to a web page)
• The numbers of new links to low trust web sites (for example, a domain may be considered low trust for having too many affiliate links on one web page).

Although there is no specific number of links indicated in the patent it might be advisable to limit affiliate links on new web pages. Caution should also be used in linking to pages with multiple affiliate links.

Why do you think Google has targeted affiliate marketing as such a bad thing?