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Yeah, for sure. But do the search engines care, especially Google in terms of PR etc?
Let's keep this one generic in nature. URI paths have no bearing on PR (PageRank).
I think the best option would be /affiliate/. Give them a link from a first level sub-directory. You could also do /sub/affiliate/. That just puts them one level deeper and possibly one PR point lower depending on the linking structure of the site.
You want to try and keep your most important content as close to the /root as possible. Affiliates would be classified as important content. ;)