I think most core files are deleted.
However most registry entries tend to stick. Say for example you install a 30 day trial, it runs out and you try to re-install. The registry entry is a part that can tell the computer...."tsk, tsk... you're not allowed to do that..." Or something not quite so amusing anyway...
One experience with 'renegade registry' values for me would be when I uninstalled "Age of Empires" from my system only to find that MSN Messenger still thought that it was on my system.
It had placed 'online play' buttons for the software because it found the 'renegade' entries in the registry.
As far as I'm aware deletion of files is like putting primer on a wall. The original program is still there underneath. But the next time the space needs to be used the computer is aware that it can 'paint' over it. Wow. Lamens terms rule. That even made sense to me!
Hope it clears up the fog for you.