A recent topic in the Development forum at Sysinternals Forums contains some information about how to use Visual C++ 2008 to create binaries that run on Windows 9x and NT. For NT, it seems to just be a matter of changing the Subsystem Version to 4.0. One might think to use the /SUBSYSTEM linker switch for this. However, when one attempts to do so, the shipping link.exe reports:
LINK : warning LNK4010: invalid subsystem version number x.y; default subsystem version assumed
In this case, the default subsystem version is 5.0, and NT needs 4.0. One can use an older copy of EditBin.exe to change this (I found the version that shipped with Visual Studio .NET 2003 to work):
editbin /SUBSYSTEM:CONSOLE,4.0 c:\path\to\your.exe
The same requirement also exists to get the executable to run on Windows 9x, but one needs to do a bit more work.
Louis Solomon has taken the time and put forth the effort to find what is needed for this, and has documented it at C/C++ EXEs and DLLs created by Visual Studio 2008 don't run on Windows 4.0 (ie, NT4 and Win9x).