Whenever I do a clean Windows installation I always ensure that I disable some of the unwanted automatic services that start up with windows, that can eat your RAM and slow the PC down.
It's also a great way to disable some of the insecure services that automatically run such as Remote Assistance on XP.
Ah yes... I've wanted to do this for a while but I'm always to lazy to click a few buttons. Don't you go to Start:Run and type in services.msc and then select the service you want to disable, right click, properties, then on startup something click disable. So the service wont run when you start windows up.
It gives a thorugh description of all services that are useful, and why you can disable most of them without impacting your fucntionality on a normal home PC (be careful with computers on networks)
with regards, to the orginal question - best way to do it is to write a custom administrative script which can be invoked after the installation