Research has shown that most users are essentially blind to ad banners. If they’re looking for a snippet of information on a page or are engrossed in content, they won’t be distracted by the ads along the top or down the side.
The implication of this is not only that users will avoid ads but that they’ll avoid anything that looks like an ad, even if it’s not an ad. Some heavily styled navigation items may look like banners, so be careful with these elements. If you design a graphic to look like advertising, you may find that users are going to ignore it.
That said, ads that look like content will get people looking and clicking. This may generate more ad revenue but comes at the cost of your users’ trust, as they click on things they thought were genuine content. Before you go down that path, consider the trade-off: short-term revenue versus long-term trust.