This will, at least on the Debian based distributions, leave the system-wide configuration files (usually in /etc) intact. If you have an issue that is caused by wrong configuration it would be better to use
Code:
apt-get purge package-name
Keep in mind that the name of the program and the name of the package package don't have to be the same (prominent example: the package chromium does not contain the Chromium webbrowser).
But I wouldn't consider a re-install to be a solution for fixing programs in the first place, since you don't know what happened to the system (why is the program not working in the first place?) and if that will occur again.
The usual way I would approach a non-working program:
1. Start it from the commandline. This way you may get error-messages that you possibly will not get when you start the program from a menu or icon, like a missing or broken dependency.
2. Make a copy of the configuration and restore it to the factory settings. In many cases you will find a default configuration file in the programs directory in /usr/share or /usr/share/doc.
3. That is rarely the case, but sometimes it is really the program that is suddenly broken, may be due to a (now fixed) file-system error or a (now replaced) bad sector on the disk. So at this point I would try a re-install.
4. If that all does not help it is time for using a websearch, may be you encountered a bug that someone has already reported, may be you find someone on a forum like LQ who has had the same problem and solved it.
5. If you still have no solution now it is the time to open a new thread here.