There are two commands that clean thing up nicely. Apt-get autoclean and localepurge, which is in sbin. Also a graphical utility to cleanup the kernel and other caches. Install localpurge and bleachbit:

sudo apt-get install localpurge bleachbit

The run terminal cleaning:

sudo apt-get autoclean && sudo localepurge

Then open the graphical utility:

sudo bleachbit