Intuitively I would like to use the Cmd key (the left one at least) in a similar way as on Mac OS. The easiest method for that is to map the LWin to LCtrl from SharpKeys. This also provides ergonimic assists for using emacs.
Some other keys such as Ins, Del, PgUp, PgDn, VolUp, VolDn and such have to be activated using a function key. The physical fn key on an Apple keyboard does not work unless deep modification be done to the system. I found that simply overriding some of the Win key shortcuts (activated from RWin) using AutoHotkeys can get us there without the trouble.
The end result is that the LCmd acts as the LCtrl; both the Alt keys remain the same; the RCmd acts partially as an Fn, and as a Win key for the rest of the scenarios; the physical Fn and Eject keys are still unfunctional.