The hidden files and folders in your home directory stores all your personal configurations and settings. In Nautilus you can reveal all the hidden folders and files by pressing Ctrl+H. If you have restored whole of your home folder, then these should be already restored.
The system wide configuration files are in
/etc (etc stands for editable text configuration). If you decide to restore the whole of /etc from your previous installation, you may want to backup the current one first, in case something in the old configuration files break something in the new install.
It is easier to re-install applications rather than restore them from backups. One way to keep track of which applications you have in which computer is by using Ubuntu One.
Alternately you can save a list of installed application from the terminal and back it up. To do this, in a terminal type:
sudo dpkg --get-selections > apps.txt
To restore the applications on the list:
sudo dpkg --set-selections < apps.txt
sudo dselect update
sudo apt-get dselect-upgrade show
Hope this helps