Making it possible to have Multiple Blogs in one application is great in some cases, I sometimes use BlogEngine more as a CMS than a blog and run a second blog as an actual blog associated with the primary site. With that said I usually run everything in separate applications as a matter of course, I like compartmentalization — one site going down shouldn't bring the rest of them with it.

Now, running mulitiple blogs has some issues — themes, Widgets and extensions need to be multi-blog-aware! When I was updating my code I realized some widgets are better left not updated. As I only run multiple blogs that are closely related in one application I decided to make some widgets unaware. Like the newsletter and tag cloud widgets, in those cases "data exchange" is a good thing!