Affiliate Program inbound links

How do you help your PR with an affiliate program?

[nevetS]

If I have a link to my site at www.mydomain.com, it's much better than having someone come to www.mydomain.com/index.php?affiliateid=something

How do you track your affiliate click throughs and still help out your PR with an affiliate program?

[ThomasB]

[webmasterworld.com...]
Should help you