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Here's one reason interest based ads might really affect your CTR.
A lot of traffic on my sites comes at "lunch hour". Surfers taking their first real break from work and wanting to get some serious PERSONAL shopping done. BUT, where are they? They're still at work. They've been using the internet for hours investigating WORK related topics.
But now they want to shop for personal items. But what ads are showing? Boring work related interest ads!
SO no clicks!
i think we've got to remember that these ads are probably making google more money, so we are stuck with them. because it allows them to put ads on sites where they'd never normally get a look in, which burns through the advertisers budget quicker.
before, they might just be competing to appear on 100 sites, but now they might have a shot of appearing on thousands. the individual click rate for any one publisher might drop as a result, but the clicks are likely racking up for google a lot quicker.
[edited by: martinibuster at 9:56 pm (utc) on May 6, 2010]
[edit reason] Removed obscenity. Keep it clean, please. [/edit]
I disagree with martinibuster:
Fwiw, I had been researching certain products and later on, on an unrelated site saw an image ad for discounted products. I clicked the AdSense ad and bookmarked the site.
* Why would some sites be affected more than others?
* Is behavioral targeting not a good fit for some sites?
* What factors make a site a poor candidate for behavioral targeted ads?
Interest-based Ads Preference 
Interest-based ads: Do not show ads based on user interest categories. Visitation information from my sites will not be used to help create interest categories.