Our site is going to be using a 3rd party affiliate program (maybe CJ) and I was wondering if having affiliate links pointing to your site is something that factors negatively in Google or Yahoo search.
Any thoughts on this, or is this indeed a dumb question?
The only way it can "hurt" is sometimes the affiliate URL can rank higher than your regular URL.
So let's say you are widgets-store.com.
You might rank #15 for "widgets."
However, if you have a really good affiliate, they might be able to boost your ranking to #8 for widgets, but your site URL might come up as their affiliate url, widgets-store.com/index.html?aid=666 or whatever.
Some people would call that a help. ;-)
Actually, if your affiliates engage in hardcore spam tactics, you could be penalized for it. That is possible.