In this context "site take-over" is a type of web advertising where the customer essentially gets to reskin the entire site. Usually means buying all the ads on the site, plus a background image and sometimes also a matching popup or expanding banner or some other in-your-face ad unit.

So it's just an advertising model, but one that focuses on high-dollar (probably direct) ad sales. If you find the right client, you can charge a lot more for a site takeover than for a couple of regular banners.