Though I've used both, I never really "got" the decisions or pros/cons that go into whether or not to choose a web site as the root entity of a new app, or a virtual directory underneath an existing web site. I have a vague idea, mostly involving "well, is it a sublocation of a master site that needs its own configuration?," but I'm not sure that's entirely accurate. I have application pools down pat, but never understood this difference.
So, question. What's the difference between a web site and a virtual directory in IIS, and why would you choose one over the other?