One of the best ways to do silent installs is to repackage the application. Windows 2000 comes with Veritas Winstall LE which you can use to port almost any application over to MSI format. Once in MSI format, the application can be installed silently by calling it with msiexec with the /i /q switches. The other nice thing about MSI deployment is on successive runs, you can use other switches to reinstall any changed files, reinstall the whole program if any files have changed... etc etc. Forthermore, if you ever get to a homogenous 2000 network with active directory, you can use the MSI files to publish the application using Group Policy.
Search the MS site for more info on MSI deployment. It is a very elegant way of installing applications and enforcing changes onto machines.