I had a thought process about OS's in the last few years and it developed in to kind of what yo are suggesting, OZ.
My idea was to have an OS that was more modular... or "plugin" oriented.
Example;
Modular OS -boots computer, has configurable settings, etc...
-Win98se Module. -When you install Win98se from the windows disk, you do so by going to your modular OS installer and selecting the "install new OS module" option, which then asks where the install CD/Drive/File is located, and you point to it. The Modular OS then installs the Win98se OS as something kind of like a DOS box in windows, but with Full-Screen options, and the ability to use an outside command to switch from wind98se back to modular OS, or a command you can execute (alt f something) to close wind98se with no complaints at all.
Of course... that leans hard towards emulation as far as I know... though I have never taken up the thought of making an OS.
In a sense, Modular OS would be the MAIN OS. From this OS you would launch other OS's and their file structure organizers as if they were other programs running... and then inside those OS's you do the same to run actual programs.....
It reminds me of the old days when you would Boot up DOS, type in win.exe, then open KingsQuest 5.
--Essentially this is the same type of model:
OS>OS>Program.
It's not ideal unless it can really work... but we all know how overmindish the windows OS's can be. Doh!
I guess I kind of rambled here... but I hope it helps in some strange twist of the word. :-)
***edit***
//Firmly agrees with Particles last comment.
