Whilst it is true that apt-get and Synaptic (or insert your favorite package manager here) make it easy to install and upgrade applications. However, uninstalling is still quite tricky specially if the application has lots of dependencies. I have been victim to getting my system borked because of an error in uninstallation - removed an app and all associated libraries accidentally. Charged it to experience and re-installed the entire OS. Good thing it is not that difficult. However, how do you prevent such from happening?

How about trying Stow, "a program for managing the installation of software packages, keeping them separate (/usr/local/stow/emacs vs. /usr/local/stow/perl, for example) while making them appear to be installed in the same place (/usr/local)."

You can read the entire documentation or you can check out the Linux.com feature on GNU Stow. :) If you have a fresh install, this might be a perfect time to run Stow.

Image from Flickr:Kai Hendry.