[kps]

Before the Linux CADETs took over with goal of cloning Windows, X11 programs routinely had configurable key bindings; poke around in /etc/X11/app-defaults (or your system's equivalent) for a few stragglers. Unix workstation keyboards typically had some form of Meta key (e.g. Sun's diamond keys) because they could think a quarter step ahead and realize that screwing up established uses of Control (i.e. ASCII) was a bad idea.

I think Qt / KDE is probably the best hope today. Since Qt got ported to OS X, there's an internal flag to use the GUI key for shortcuts instead of Control. If this flag were user-configurable it would solve a large part of the problem; perhaps the latest MacBook ‘Pro’ will generate enough refugees to make it happen. In the interim, KDE apps at least have individually configurable key bindings.