Affiliates and SEOs don't always get along, but at the same time, some of the best affiliates are the best SEOs and some of the best SEOs are the best affiliates. They often go hand in hand, but there is often a disconnect between the two.
Many SEO affiliates look to maximize their links by making sure those that link to them via affiliate URLs also pass link weight along with it.
An excellent "supporters" thread (meaning, you need to pay to see it) at WebmasterWorld talks about strategies to get the best of both worlds. To get people to use your affiliate program, pay them and track them, but at the same time, keep link weight passed by those links.
In short, ZydoSEO, a preferred member talks about three strategies. I will mention them shortly here but feel free to check out the thread after becoming a supporter. (Note, I am not making an affiliate commission by saying this :))
(1) Use normal tracking URLs, cookie the click and commissions and then 301 redirect them back to the main URL. Once the information is passed to the cookie, it should be fine to 301 redirect those links.
(2) Use search engine friendly based tracking URLs, still you want to cookie the click and then 301 redirect them to the proper place.
(3) Or you can try the rel=canonical element, instead of a physical redirect, you redirect search engines that way.
The canonical method is probably the easiest route, but not all search engines fully support it yet. Google does.
Forum discussion at WebmasterWorld.