A lot of programs when imperfectly packaged will leave behind folders. Either empty folders or with configuration data. Just delete them manually if their presense bothers you.

You can also remove programs using "apt-get purge" from the command-line, which is a more "complete" removal of programs than "apt-get remove" (what the app managers use in the background for removal), but that's not always guaranteed to remove everything either, as far as I know. However, if the program is properly packaged, whatever's left will be just folders with config data and the like.