It's a shame the ad bits got the most attention in this article. I think his brief mention of creative functionality segmentation and fee-based services is really where it's at, unless your user really doesn't care about all the ads. Most people really hate that stuff, and even if they'll put up with it, you have to be offering something pretty darn good, that no one else offers without ads or with better features. Otherwise they'll jump ship.
I also think there is something to be said for a more specialized campaign. The difficulty is these tend to only be feasible on larger sites with lots of traffic, but I do think there's room for smaller advertisers to be paired with smaller sites and do more customized campaigns. An excellent example of custom ad campaigns can be found on http://www.penny-arcade.com/
where often times the artist for the comic will actually draw the ad, making the ad very well integrated with the content. They also only agree to advertise things they actually like, so automatically there's a level of trust that brings down a clicking barrier for many people. People know that not only can they trust there will be no adware, spyware, etc. if they click, but that also the service/product is likely to be of interest to them if they like the Penny Arcade comic and blog. Now those guys have massive amounts of traffic and are a bit of a unique case, but again I think there is room for more of that and it's really just a matter of hooking up with smaller advertisers and working out what they're willing to pay.
I almost envision a site like GetAFreelancer.com or Elancer.com where you have advertisers and site owners, and each are making themselves available or bidding on each other's opportunities. Site owners can make a per-click or flat time-based bid on an advertiser's product (run an ad on the front page for 1 week), or advertisers could bid on a site they want to be on. Multiple bids could be submitted and compared, just like Elance, etc. Private messaging, portfolios, stats, reviews, etc. would backup each vendor's bids. Discussion between parties would involve the customizations desired for the campaign or site, and a bid would be accepted once the negotiation was solid. The site would then moderate and record the traffic and completely handle the transfer of money through an escrow system, or similar. This is basically ad and site matching the Elance way. Actually, anyone know if something like this already exists? If not, it damn well should!