DOH!
For that you need to install the MS command shell (which is included on H/PC's but not PPC's) and a console driver. You can find both of those at the
SymbolicTools website. This gives you a command shell from which you can execute all the usual commands (including batch files) so you can just write a normal DOS/WIN style batch file and have it execute directly in WinCE (the file association is setup automatically).