I have a very simple script for cleaning out apt whenever I feel the need.
I have it in /usr/local/bin/clean
So I just type clean into a terminal and it automatically clears out a few places that I want cleaned.
Of course this is not all of the things you should be cleaning out. The link to Make Tech Easier has some good suggestions.
#script to do a quick apt cleaning
sudo apt-get --purge autoremove #removes unneeded packages that were installed to satisfy dependencies along with their config files.
sudo apt-get autoclean #removes obselete files/packages that can no longer be downloaded
sudo apt-get clean #removes the downloaded packages to free disk space