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IMO, there is not a best practice; there are goals, and ways to acheieve them. ;-)
As far as showing affiliate links, there has long been speculation that showing affiliate links can get a site in trouble or somehow dampen its rankings. However, there are plenty of sites out there that make no effort at all to hide aff links, yet rank very well for lots of searches throughout various levels of the site.
IMHO, the issue has never been about being an affiliate; the issue is making sure that your site provides unique content and added value versus what is available elsewhere on the Web. If it doesn't, why would any SE want to show it versus existing alternatives that are already doing the same thing?