I've worked on one site before where I redesigned the entire site from scratch and was able to get an above average CTR on a daily basis. However, I just launched a new site, using the same knowledge and methods, and I'm barely getting CTR. I attribute most of this to the content difference between both sites (pet adoption/pet help topics vs. music news/reviews/interviews). Site looking for review right now: www.acclaimedpunk.com (Other site is www.sandiegopetadoption.com, but that one I'm fine with)
The answer lies in the difference between the ad placement and formats on the two site, on the succesful on you have a large rectangle placed prominently - no one can miss it. On the music site I had to look twice times before I even noticed the scraper on the right. The half banner in the content would seem like a good idea, but people have to scroll to find it and they have to read through your content. You've got nothing for the acceidental surfer with no interest in your site who just wants to exit your site as fast as possible (by clicking an ad).
Good point. I am probably going to be tweaking the organization of the main layout on the home page soon. Definitely forgot about the scrolling aspect.