I ran into an instance just this morning where I was trying to install a prototype of an app on someone's laptop, using a virtual-python setup, and I ran into problems due to packages being in the system-wide site-packages that were in the way of what I wanted to install in the virtual-python environment.
I ended up removing the symlinks from the virtual-python's site-packages dir, but perhaps a good wiki page somewhere would be a collection of big long one-liners that remove Python library packages from various operating systems. For instance, I would use a big long apt-get remove ... line on Debian systems :)
In working-env.py by default I leave out site-packages entirely (though there is an option to include it). Then you don't have to remove anything, since nothing at all gets copied over ;)# Ian Bicking