Unfortunately, as a site owner there is not a great deal you can do to protect your site..directly.
Parasites go after the promoted site not the affiliates sites as such, they prey on PPC, Organic SEO, paid listings the lot. It just happens that the affiliates suffer along with everyone else as they overwrite your tracking at the merchants end.
For example, say you promote merchant XYZ.com, a system like (deleted, no specifics please) targets their domain name and trademarks, not you links, therefore when a person clicks your link, and ends up on XYZ.com your tracking is hit at that momment....nothing to you can do to stop that.
Partial Solution : Don't promote merchants that work with parasitic marketing systems.
That stops some systems, however for (deleted) and others like them it's not going to stop all parasitic action, as you have other affiliates who use their PPC engine to still target the brand names and so forth. Then it's down to the Affiliate manager to spot and eliminate such people.
Certainly the first step is work with merchants who are parasite free.
Hope this was helpful.
[edited by: eljefe3 at 4:26 am (utc) on May 4, 2005]