[eluser]Nick_MyShuitings[/eluser]
I run a different route, I run several sites off of an identical systems folder. Reason being is that the sites are almost clones of one another. Views and specific files are modified from one to another, but the controllers, libraries, and such are identical.
In my case it made more sense to keep system under one version control repo (Hg) and each application in its own repo (Hg).
(the logic was also compounded by how Dreamhost makes you do file structure... this way I can update each site indiv, and push system patches (like 1.72 to 1.73) seperately.