One problem that can leave your system unstable is dependencies or orphaned packages leaving after you uninstall a package.
This problem can be solved by installing a tool called debfoster. It tracks what you have installed and ask you to uninstall dependencies files when you uninstalled a program.
//install
sudo apt-get install debfoster
//help
sudo debfoster --help
//create initial keeper
sudo debfoster -q
//system to conform to keeper
sudo debfoster -f
//check orphaned/dependencies files
sudo debfoster
More information: using debfoster in practice