I'm having to deal with placing ads on a website I'm working on for a client.
Is it best practice to always have a dedicated column for the ads and potentially blank space below the ads as you scroll or can/should you for any reason wrap the content around the ad space?
From a user perspective, content and non-content should be as distinct as possible. In the mockup on the right I can see some potential for an ad to appear as though it were part of the content rather than an advertisement, which can at times be quite dangerous; I can personally attest to a great deal of frustration with various file-sharing sites with ads that feature prominent "Download" buttons very close to the less prominent REAL download button.
I would also say that I prefer content to have a consistent width even if it means some space is wasted. I can't say for sure that this is "best practice" or anything, but as an example you can scroll down on this very site and find plenty of empty space below the "Hot Network Questions" area in order to keep the content at a fixed width.
The biggest problem with ads is that they are poorly written and often full of animation so they are always slow to load. On completing the load, they do the worst thing possible to you users reading content... they move it.
Since ads are largely out of your control, the only thing you can do is segregate them from your content. Otherwise, chasing content around the page as multiple ads and slow graphics load and shuffle everything around drives many a user to the next website.
