Affiliate software is different to CMS software. Please re-open my question.
Looks like that question is over six years old (from 2011), and since it's seeking a recommendation for software, which is considered off-topic for this site, it can't be reopened.
If you check our Help Center's FAQ's on what topics can I ask about here, you'll see:
Recommendations for sites and resources -- Questions that ask for recommendations of external websites or resources attract lots of self promotion and spam answers. In addition, answers to such questions quickly become out of date. Such questions are closed as off-topic.
Based on the sentence
I'm not sure what CMS or shopping cart software to use yet, but it will need to include an affiliate system to allow advertisers to push customers our way, it might appear that you were looking for a CMS that includes an affiliate system, which is why John likely marked it as a duplicate of our community wiki that's a catch-all for any questions related to finding a CMS.
I have unmarked the question as a duplicate and re-closed is with the more appropriate reason:
Questions asking for recommended external websites, tools, resources, and software are off-topic as they tend to attract opinionated answers and spam. Recommendations for software are permitted on Software Recommendations, but be sure to read their quality guidelines before posting there.