I'd just like to add that for now, the auto-generated links from ISBNs are not "affiliate coded". So we don't make any money from those links.
However, with the ongoing hard times in the Internet economy, we do anticipate adding some forms of advertising to the site in the near future. One thing that we will do is make sure that ISBN links are affiliate coded.
I would of course view it as inappropriate for people to insert their own affiliate coded links into the Wikipedia.
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Some abstract thoughts on these matters:
1. Advertising must not interfere with the content of the encyclopedia. There must be a "Chinese wall" between the two. This is ensured by the fact that the content portions of the pages are always editable by anyone. Advertisements should be separate from content and must be clearly advertisements.
2. Although links to booksellers are a natural fit, a natural feature that people like _anyway_, some may feel that they blur the line to some extent between advertising and content. The important thing here is that even as advertising, automatic book links should be vendor neutral, and I would also support including some kind of library link there, too.
3. Amazon.com is the easiest (to my knowledge) affiliate program to work with. But, Amazon.com is controversial in the free software community for their patent activities, most notably their monumentally stupid and offensive "one click" patent, which they used to restrict competition from Barnes&Noble. I'm sensitive to those concerns.
4. My current thinking on advertising is that people who are logged-in should have ads turned *off* by default, although if they want to help fund Wikipedia, they can turn them back on and make an effort to click through and buy stuff.
5. I know the introduction of advertising will be controversial with some people, no matter how carefully and sensitively we do it. Those people are invited to step forward and pay for Wikipedia out of their own pockets if they like. :-)
--Jimbo