Personally, I have a strong preference FOR affiliate links / referrals over other kinds of advertising, simply on the basis that they're more targeted, and more likely to be relevant to me at that point in time. If I click through to a store based on your content, I'm generally pretty happy if my referer gets a little piece of the action.
That said, it's also pretty obvious affiliate links can be done badly, and there's a nice slippery slope in there somewhere. I actually like how Tim Bray does it on his blog - when he posts affiliate links he points it out explicitly (I think they're usually his partner's) and provides non-affiliate links as well so you can opt out if that's how you feel.
In general, more transparency is better, as usual.
That said, it's also pretty obvious affiliate links can be done badly, and there's a nice slippery slope in there somewhere. I actually like how Tim Bray does it on his blog - when he posts affiliate links he points it out explicitly (I think they're usually his partner's) and provides non-affiliate links as well so you can opt out if that's how you feel.
In general, more transparency is better, as usual.