Apologies for the obtrusiveness of the new ads. You'll notice a banner ad at the top of the main page as well as a box ad in between the story content and the comments when you click on the "Entry Link" or "Comments". While the ads are likely here to stay in one form or another, the integration of the ads with the rest of the site will be improved.
I'm not sure exactly how or when that integration will work, but the powers that be have informed me that they are working on it as we speak. I have assurances that there will be no pop-up ads, and you'll know as soon as I do what the eventual fate of the existing ads will be.
Thanks for your patience as well as your continued patronage. I'll keep you posted as to the status of this obvious hot-button blogging issue!