The easiest method is to create an MSI. Here's a link to read about it: http://www.microsoft.com/windows2000/techinfo/administration/management/wininstaller.asp

 

You can do this very easily with a batch file. It already sounds like you know how to make the registry entries ok so I won't go into that part of it.

For example, if the registry file is "viperben1.reg",
the batch file just needs to be "regedit /s viperben1.reg"

To delete an entire key it would be something like:
REGEDIT4
[-HKEY_LOCAL_MACHINE\Software\Microsoft\Office\8.0\Common\Assistants]

Would delete Assistants key and everything below it

To delete just a single entry it would be something like:
REGEDIT4
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run]
"MSConfig"=-