What distro are you using? The reason I ask is that I also have repaired my gnome desktop after breaking it, and if we know which distro you are running we can help provide the correct cli commands. For instance I broke gnome under Debian, so from the command line as root I ran:
# apt-get --purge remove gnome-panel gdm
# apt-get install gnome-panel gdm
Now with this, I lost all settings and had to add all of the customized gnome settings because it completely removed gnome and then reinstalled a fresh version. But it did completely fix it.