I know of only one website that does ads right: the Penny Arcade web comic. I admit I haven't gone there in years, but when I did, their ads were always products they approved of (usually computer games), in the style of the web comic, in a way that fits the site, and made by them, so no malware. This makes it less intrusive, but also a powerful stamp of approval, that I suspect makes it far more effective as an ad. This is better for legitimate advertisers and visitors, although it does mean extra work for the site, of course.