I just had a thought I figured I'd share with the class. Say you've got an affiliate link like http://newmoneymakersite.com/index.php?aff=myname (not a real affiliate link) It seems theoretically possible that if a page gets enough backlinks it should rank in the SEs. So shouldn't it be possible to get your affiliate link indexed in the SEs? So when a user searches for "new money maker site" your affiliate link comes up #3 or even #2 behind the actual site? In effect you'd have google, MSN, and Yahoo sending hundreds of uniques to your affiliate link every day. We know that SEs finally wised up and most are now indexing query strings so a page like my affiliate link above should get picked up intact right? Thoughts, theories?
I have seen this happen and affiliates do get a big boost in commission. There isn't much that can be done to stop it - good luck if you can get a link listed! I think if the affiliate has the links logging a hit and then redirecting to their homepage using a 301 redirect then the affiliate links won't be recognised as being different to a normal link and won't appear in the SERP's.
keep in mind that affiliates will get a boost in commission but still you wil be having a share of the pie.