Does Affiliate Linking Help or Hurt?

Does having an affiliate program where affiliates have a direct link to your web site help or hurt your link popularity? Are they more or less relevant because they are an affiliate?

Depends on how the link is contructed. If they all link to the same pages in the same way then they might help.

If each link has an &id=xxxx part in it, then they will cause you problems as the same content will appear to be accessible via several different URLs, and you know that Google filters "duplicate content" out of search results.