The only time there's really a valid reason to complain about affiliate links is if you're rewriting links posted by others; and even then IMHO disclosure is enough to clear you. Otherwise, affiliate links are serving their purpose properly (encouraging bloggers to post links to Amazon; and Amazon compensating the bloggers for the referral).
I would find a follow-up post discussing the numbers re: Amazon Affiliate click-through and purchase rates from a story hitting the front page of HN more interesting than yet another "here is a list of books that you should read" post, or is that a little too meta?