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Now domain.com/index.php will look exactly the same regardless of variables in the link, so if I have 1000 affiliates, then the search engines may find 1000 "pages" with identical content.
I did some search on this topic here at webmasterworld, but all I found was ancient discussions. The solution that was mentioned was to scrap the variable all together and track affiliates by referrer url instead. The limitation would obviously be that each affiliate must notify me of where his traffic originates, else I can't track him.
Is this considered the best solution nowadays, or what is the view on this?
Of course you could look at different software that would provide you with different tracking capabilities, but if you are worried about dupe content, make sure your affs change their page.
OR you can put your affiliate code after a # sign. So the URL would look something like this: