With most Linux distros now using GNOME 3.10+, here are a few commands on changing the look and feel of your desktop using gsettings. Other CLI methods exist such as the popular GNOME tweak tool and Dconf.
Add apps to favorites bar
$ gsettings set org.gnome.shell favorite-apps "['google-chrome.desktop', 'evolution.desktop', 'nautilus.desktop', 'libreoffice-writer.desktop', 'libreoffice-calc.desktop', 'firefox.desktop', 'gnome-terminal.desktop', 'vlc.desktop', 'jitsi.desktop', 'gedit.desktop', 'gcalctool.desktop']"
Change show date and clock format
$ gsettings set org.gnome.desktop.interface clock-show-date true
gsettings set org.gnome.desktop.interface clock-format '12h'
Change background picture
$ gsettings set org.gnome.desktop.background picture-uri 'file:///usr/share/backgrounds/gnome/Sandstone.jpg'
Those are just but a few of the settings available for you to tweak. To see all of them, type:
$ gsettings list-keys