You can write your logon batch file to check the type of Windows OS they have, then do specific tasks based on that. I think the way we do it is we check if the have a "c:\Windows" or "c:\winnt" folder. If windows, then it's a 95, 98, or ME system. If winnt, then it's either NT4, win2k, or XP.
For us, this will work since we don't have any custom installs where a win2k box might have a windows folder instead of winnt. All out batch scripts do right now though is they map network drives and load the web browser to a news and info page... yes, at every logon, and it is annoying to have the browser open all the time....