I think this post about page design is one that should have been made 3 years ago–many thanks to Graywolf for putting it out there. The problem most people have is that they don’t do much thinking about ads until after they finish their design template.
So of course they then have to “fit them in somewhere”… and usually that “somewhere” is somewhere where they don’t “clutter up” the design. The problem being those “clutter up” spaces are usually where the heat map turns orange or dark orange.
The thing is, if you work hard at it and focus on ads in the beginning, you can put them in obvious, ‘obtrusive’ places without losing as much of the site’s aestheticism. Yes, you’ll lose a bit; it’s a tug of war.
Bottom line: are you in this to make money or aren’t you? If you are, check out Graywolf.