AT is an option - you need to be careful how you set it up though because you may not be able to access some network drives and resources. Make sure the schedule service is started, and make sure it starts when the system reboots. You can set it up so that it logs in as you (which has more network privileges) or as the system account (which is less privileged).
Also consider grabbing winat (on one of the NT resource discs I think) which gives you a slightly nicer gui front end.
e.g to run master.bat at 1am every morning:
at \\<MACHINE> 1:00AM /every:M,T,W,Th,F,S,Su cmd /c "e:\batch\master.b
+at > e:\batch\logs\master0100AM"