These commands work with Gnome 3, Unity, Cinnamon, Mate desktop, and also the old Gnome 2 desktop(if you still using it).
Why we need to type some commands to get it done instead of a Gui tool ?
This is important to ask in such situation. In Gnome 2(and Mate today) all the these settings can be easily changed using build-in Gui tool called Appearance Preferences. Unfortunately in modern desktops such as Unity Gnome 3 ... we have Gui tools that can do the same, like Gnome Tweak Tool, Ubuntu Tweak, or MyUnity, but with limitations. It means that "Appearance Preferences" (Gui tool to tweak Gnome 2 and Mate) is powerful than any other tweaking tool.
Since "Appearance Preferences" doesn't come with all desktops except Mate, The command line will be the only replacement.
1 - Change GTK Theme
Unity, Gnome 3 Shell/Classic, Cinnamon
gsettings set org.gnome.desktop.interface gtk-theme "Mytheme"
Mate
mateconftool-2 --type=string --set /desktop/mate/interface/gtk_theme "Mytheme"
Gnome 2
gconftool-2 --type=string --set /desktop/gnome/interface/gtk_theme "Mytheme"
2 - Change window theme (Metacity)
Unity, GNOME 3 Classic (Metacity), GNOME 3 Shell (Metacity > Mutter)
gsettings set org.gnome.desktop.wm.preferences theme "Mytheme"
Cinnamon (Metacity > Muffin)
gconftool --type=string --set /desktop/cinnamon/windows/theme "Mytheme"
Gnome 2 (Metacity)
gconftool-2 --type=string --set /apps/metacity/general/theme "Mytheme"
Mate (Metacity > Marco)
mateconftool-2 --type=string --set /apps/marco/general/theme "Mytheme"
3 - Change Shell theme
Gnome Shell (user-theme extension must be enabled)
gsettings set org.gnome.shell.extensions.user-theme name "Mytheme"
Cinnamon
gsettings set org.cinnamon.theme name "Mytheme"
4 - Change GTK color scheme
Unity, GNOME 3 Shell/Classic, Cinnamon
gsettings set org.gnome.desktop.interface gtk-color-scheme "bg_color:#e9efe9;fg_color:#444444;base_color:#ffffff;text_color:#333333;selected_bg_color:#6666cc;selected_fg_color:#eeeeee;tooltip_bg_color:#222222;tooltip_fg_color:#dfcfcf;link_color:#cc0099;"
- Reset color:
Mate
mateconftool-2 --type=string --set /desktop/mate/interface/gtk_color_scheme "bg_color:#e9efe9;fg_color:#444444;base_color:#ffffff;text_color:#333333;selected_bg_color:#6666cc;selected_fg_color:#eeeeee;tooltip_bg_color:#222222;tooltip_fg_color:#dfcfcf;link_color:#cc0099;"
Gnome 2
gconftool-2 --type=string --set /desktop/gnome/interface/gtk_color_scheme "bg_color:#e9efe9;fg_color:#444444;base_color:#ffffff;text_color:#333333;selected_bg_color:#6666cc;selected_fg_color:#eeeeee;tooltip_bg_color:#222222;tooltip_fg_color:#dfcfcf;link_color:#cc0099;"
- Reset color :
Note : You can also try to use some other tools like dconf-tool or gconf-editor