I've recently spent a lot of time on Boston.com tracking Red Sox free agency rumors. I've been very impressed with Boston.com's revamped sports section and blogging efforts (the best I've seen for online newspaper sources) - but I have also been struck by the advertising on their homepage... which is rather untraditional compared to other branded, highly trafficked websites. I've written about aggressive branded campaigns before - using the New York Post as an example. Boston.com takes the opposite strategy: lots of varied ad-sizes scattered throughout the page.
Take a look at a screenshot from Boston.com and the Wall Street Journal below. Boston.com has two 180x90s beside their logo, two 235x60s on the left column and a 300x250 on the right. Honestly, there isn't much room for content between all the various units. The Wall Street Journal however, has two matching, rich-media units and a smaller banner in the header promoting WSJ subscriptions. The WSJ screenshot is poor because it doesn't capture the full horizontal ad-unit (it's being collapsed).
In the long run, I imagine that the Wall Street Journal is most effective for the brands... and consequently for the publisher. It's certainly the better user-experience. Fill rate for those integrated, rich campaigns are likely below 100% - and that's perhaps when the Boston.com strategy is best served: as filler.