Will they accept a web based application or one with a non-Win32 GUI (if you use Tk for example)?

Serving web-based applications on Win9X is fraught with peril. There are known memory leaks that will prevent high uptimes. An architecture where the Win9X box is both the server & client sounds too fragile to me. How complicated will the startup process be if the box freezes and the end-user has to reboot?

Also what exactly is so special about this business that it can't use something like Peachtree accounting? The basic accounting package costs around $90 and may be all you need.