I actually use Linux, OS X and occasionally Windows at work. (I work on Qt, so I need to be able to test bugs and features on every supported platform.) I use the same keyboard for all of them, on a KVM. It's not so hard to get capslock to be the control key on all of them. (On Linux though, that means remapping it on both the console and in X11 and Wayland globally, not just in some desktop environment's control panel.) But then after using OS X I have grown to like the idea of keeping control (as used on the terminal) separate from command (as used to copy and paste text and other such things, even in the terminal window). I'd like to find a way to make that consistent everywhere. I think I will find a way on Linux. But first I want to have an ergo keyboard with a real command key. (Thus the ergodox, with its customizable firmware.)
For now though, on a regular ergo keyboard, capslock is control, and control is also control on Linux and Windows, whereas on OS X I map capslock to control and control to command and the windows key to command, so that I can develop portable muscle-memory: I use the same key for control-C or command-C regardless of OS when I want to copy text, and the same capslock key for control-C to stop a running program, for example. And the windows key is closer to where the command key is on a MacBook Pro, so if I hit that one by accident it still works, whereas the windows key has no other use on OS X.
It IMO doesn't make as much sense to remap the windows key, because it has its own uses in various Linux desktops and window managers now. So, the more bucky keys, the better; it seems I actually use 5 of them now: control, command, alt, window and compose. Oh, and shift, of course. The window key is still the least useful though. Can't decide whether I prefer using window-mouse-drag or alt-mouse-drag for moving windows around. There is some inconsistency about that between openbox, awesome and weston.
I was using a model-M at home, with no Windows key, but my wife complained that she couldn't sleep, so that's the trouble with that. But then I had to try to use the two alt keys more effectively. The right one has to be compose if you need compose, whereas if you also have a menu key, you could use that for compose. I live in Norway now, and don't want to get used to Norwegian keyboards because they are too different (lots of odd and unnecessary changes), because I don't actually write much in the Norwegian language, and because I will never be able to switch completely due to having lots of old hardware. So I use compose for writing the 3 extra characters ø å and æ. I think it's an intuitive and extensible way to handle all the accented characters, and everyone should have a convenient way of typing them, even if they are only needed in rare cases.
After I switch to ergodox, I wonder if it's going to get really hard to use other keyboards though.