Comment 52 for bug 1002187

Well, the intrusive behaviour you describe - removing files belonging to libgl1-mesa-glx - simply sounds unacceptable to me, and I can't help thinking that you ask for trouble by installing the driver directly from the nvidia site.

I am using the nvidia-304-updates package, provided by Ubuntu's "restricted" repository, together with the latest version of skype and skype-bin. It just works, without any manual workarounds of any kind.