potentialgeek - 7:44 pm on Nov 17, 2011 (gmt 0)
Nearly every major site uses display ads including a leaderboard (top) and a 300x250 unit (right, near top). These are nearly always above the fold - the advertisers require them to be above the fold - so they'll be seen. However, these ad positions are conventional; therefore they do not interfere with user navigation. Users may ignore them, but they aren't lost on the site because of them. Google is not going to penalize those sites.
The signals which will likely trip the next ad filter are a combination of:
Ad appears above the fold AND it's a text ad AND it's right next to/above links AND/OR page has high bounce rate
I think we've all seen aggressive MFA sites which Google would like to target because the ads confuse users into thinking ad links are page links... or tons of ad links appear before the content (e.g., 2 or 3 units above the first paragraph).
Remember when Matt Cutts was asked about Suite101 after it was Pandalized? At the time it had tons of ads on each page, including where you'd expect a navigation menu (left column).
I don't know if I've ever seen a legit site that misused text ads.
There is a big difference between display ad networks and text ad networks. The difference is "editorial" control. The display ad network I'm on requires approval of ad positions, including making sure they're above the fold. Google Adsense, etc., on the other hand, do not review and do not approve ad positions.