Ads are basically the necessary evil on most websites. They can kill a really great design, but if you can’t afford to maintain your website then who cares about the design? They are especially important for online news sites or resources and need to be taken into account early on. It’s best, when possible, to consider ads in the wire framing process when you are building your site and business. It’s good for us designers to just buck up and realize early on that we will need ads to sustain company profit. Ignorance is not bliss a few months down the road when trying to squeeze them into a design 🙂
Personally, I’m a fan of ads placed above the main navigation. I think it allows the advertiser the most bang for their buck, while not getting in the way for users. I hate when I’m trying to read an article and I have to navigate around the ads to do so. I am likely to admire the ads above the header when they are not in my way!