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I don't know much about the various types of affiliate software, so I'll leave that to the experts. But I can tell you what Google says (at least publicly) about the "SEO value" of links on the sites of your affiliates. At an SMX conference, Matt Cutts (Google's head of web spam) said that Google essentially knows how to "handle" the major affiliate networks but that affiliate marketers may want to add nofollow tags just in case. (See the YouTube video.) What does "handle" mean? I would suggest that it's Google's aim NOT to have such affiliate links pass "credit" to the original site because Google views them essentially as paid links or links that are not placed naturally and editorially. Cutts suggestion to use nofollow is a way to stop this from happening for any smaller affiliate network that Google might not know about. Short version? I'd be highly skeptical of any claim that affiliate links help your "SEO." Sounds like snake oil. Given enough time, I project Google will become good enough that any link that is not 100% earned (rather than built) through good old-fashioned marketing and PR will not help websites (and may, in fact, hurt them). Moz also has a good post here with some affiliate SEO suggestions and further commentary on the issue.

Mike, this comment you made is correct: "my understanding is that Google disregards everything after the "#" so there shouldn't be a duplicate content issue." If you do somehow see one of these getting indexed in Google then you have an issue, but I have not seen this happen.

In the olden days, before search engines, our elders judged links based upon the traffic they would send. You have to consider that someone is going to click on that link. Maybe that set's the site up as an authority in one person's mind. Eventually they will run into other people that are like-minded . Maybe these people go out and publish something, with followed links, from somewhere pretty nice. It may be a long shot, but Wikipedia tends to rank well for informational queries. The links that may follow would help later. You have content on a site with pretty high visibility. I would ask you, how is this a bad thing?

Practically speaking, in my experience the difference ranges from a 1:1 relationship to a 1:8 relationship, which is a huge spread. A lot of SEOs I know, including our tools developers here at Moz, have shown an interest in Grep Words. Might be worth checking out if you were interested.

Yeah I noticed the same even for paid customers. At first I thought it was for unpaid customers, as there is a way to setup your profile via someone requesting to set it up, but not get a followed link. However checking paid aka Verified accounts it does not have a follow link, really interesting..

Unfortunately this company is one of the largest - they're just raking it in.  So not only are they ranking high but the pages must be converting well for them.

Hi Peter, Thanks for the feedback.  You're probably right that testing the waters is not worth the potential long-term implications.  This certainly helps. Regards, Mike

You can check how often Google is crawling your site through Webmaster Tools > Health > Crawl Stats

I can't say for sure if this would hurt you, but I know that we saw a definite decline in ROI after after an extended period of doing nothing but press-releases for our link building. It's probably a good idea to mix things up and go after some different link types if you can. Our strategy is to go after the high-value, high-investment links first. Then read and comment on relevant blogs, submit to niche directories, bookmark content, post guest-blogs, and join new social media communities where it makes sense.