Generally, the hidden files contain settings and data specific to the
application, but not the programs themselves. I think deleting the hidden files
is a bad idea, if you plan to re-install the applications.

To make a list of all your installed packages use this command:
dpkg --get-selections "*" > Desktop/applications
(it creates a text file called "applications" on your desktop.)

To install all the packages, use these commands:
sudo apt-get update
sudo dpkg --set-selections < Desktop/applications
sudo apt-get -u dselect-upgrade

Before doing the re-install, I usually go through the text file and delete most
lines, because it will contain each package in a default install, libxxx files
which are to resolve dependencies, and stuff I installed and then lost interest
in. It's not a trivial task, because the file will probably contain over 1500
lines.