Directories to backup user and apps settings

/home

dpkg --get-selections > ~/my-packages.txt 

to build up a list of everything installed (or removed) on your system. It will be saved in your home folder as my-packages.txt. Once you reinstall, run 

sudo dpkg --set-selections < ~/my-packages.txt

(assuming the file is placed in the same location again) and then 

sudo apt-get -u dselect-upgrade 

to start installing packages. You'll want to also back up 

/etc/apt/

and restore it on the new installation to ensure that any extra software you may have installed is still able to be installed again.