I love the fact you can set-up a perfect working environment, with outline, brief, email traffic, research folders (containing anything you like) and of course the draft text, all in one place.
Here is a research folder of a review paper I am working on right now. All the relevant PDFs are at my fingertips.
I also like to use the Template feature of Scrivener. When I have found a set-up that I think I'll need again, like that for grants, review papers, formal reports, I'll save it as a template so I can re-use it next time.