I've go the same problem and here's what I found:

All my NT Workstations have the environment variable 'OS' set to "WINDOWS_NT"

So that I can control certain batch files....I've also put the OS=DOS in the autoexec.bat of each station running DOS (I only have 15, so it was an easy task) This allows the following to be used in batch file:

IF %OS%==Windows_NT  GOTO NT
IF %OS%==DOS GOTO DOS

!the apps have not been tested for Win95/98
!OS_WARN.BAT just pops-up a 'WINDOWS 95/98 not supported' error
@CALL OS_WARN

GOTO END

:DOS

! put DOS commands here

GOTO END

:NT

! put NT commands here

:END

I've used this most commonly to support old code where reports depend on LPT1 being captured and pointing at the correct printer.