The Windows source code
is already available from Microsoft Research Laboratories; to what extent, I don't know.
Microsoft makes its source code available to Universities at a no charge basis. However, it seems to be unlikely that this would encompass all of Windows CE/9x/NT. I would really like to know if they make kernel available as source, as that seems to be the place where most of the improvements to Windows can be made.
If anyone has the exact license agreement that representatives from these Universities must agree too, I believe it'd be fascinating reading material. Everything that comes out of modifying the Windows Source would, of course, be nonprofit, but what exactly could be done with it? I'm sure the license is quite restrictive, but that remains to be seen.