The simple rule is: If the article is good and people will read it to the end. Be honest with yourself. Put the ad AT THE END of the article. If the article is very short or poor quality. Again be honest with yourself. Put the ad AT THE TOP of the article.
Right smak in the middle of the article (about.com is a great example). The medium rectangle format usually brings a good CTR>
An article can be great whether its sort or long depending on how the reader finds it. Also, remember that many people do not like having many more than 400 words or so on a single page. If an article is 1500 words long for example, it will be over 3 pages.
I find the skyscraper to be the best performing ad - much better than banners or cubes. The rule is to experiment and see what works - not take comments about news article quality as gospel.