After a while of using linux you can end up with a lot of downloaded but not installed packages and/or unwanted dependences, which can take up a lot of disk space.
It is quite easy to clean these up however.
In Debian based systems that use the apt package manager you can simply type:
bash$ sudo apt-get autoremove ; sudo apt-get autoclean
In arch linux using pacman to clean the package cache of packages that are not currently installed:
bash$ pacman -Sc
And to clean the entire package cache:
(Warning: Only do this when certain that Downgrading Packages will not be a necessity, as pacman -Scc removes all packages from the cache.)
bash$ pacman -Scc
Some programs such as Ubuntu Tweak are being developed to help with modifying and generally cleaning up the system so keep an eye out for them.