The answer is... dun dun dun dah... it depends!
I know, really useful. Some distros package managers will clean up all the old files for you. Others will only remove explicitly what you say unless you pass it some options to remove all unused files. Some distros will delete the old kernel when you upgrade using their package manager but not when you compile your own. In Debian, there are tools like deborphan to help find packages that aren't used by anything else. Then you can safely remove them. As for other file types, I'm not sure (I think deborphan also checks the default config files in /etc).