I could imagine using Wireframesketcher to just draw sketches within a projects. I have done this before, not with Wireframesketcher though, but with normal text files.
But so far I have used WireframeSketcher mostly as a separate tool. At the moment I even have a dedicated eclipse for it, as I was test-driving the latest milestone of Eclipse 3.6 (Helios) (btw, it works, if you're wondering if your plug-in is compatible).
The main reason for this is that the projects I draw wireframes for at the moment don't require me to document/backup them on our corporate servers or revision control systems. So I prefer to keep things separated. It's mostly for my own designs for some features or to showcase things and discuss them over meetings.
I haven't really used it to design a complete application or website so far, except smaller size websites at Macquarie University.
I would probably start using it more and more in design phases and be more and more thorough with my coverage as time goes by.