You could try, as root or sudo, "dpkg-reconfigure gnome" (assuming you have the metapackage gnome installed. if not, maybe "dpkg-reconfigure gnome-core"). The commands are to reconfigure gnome.
To open an application installer from the command line, you could try "sudo synaptic", or "gksudo synaptic" to open a gui application installer. To install programs from the command line, run "sudo apt-get install". Or, for an ncurses interface, in the terminal enter the command "sudo aptitude" (note, aptitude is reputably a better application installer than is either the application installer, synaptic or apt-get, but only if it is used exclusively; so, if you still plan to use any of the others, it may be best not to use aptitude).
If nothing else works, and as a last resort, you may simply wish to remove the gnome hidden files from your regular user directory, which, upon reboot, should (I think) be recreated back to the default settings. These hidden files are usually (see code below):
or
Note, above, "user" refers to whatever your regular user has been named. Also note that hidden files always begin with a period (
.)
disclaimer: Note, I use Debian, so, perhaps, some of what I say may not apply to Ubuntu. The sudo stuff, which I don't have set up on my system (I just use root when I need to do system stuff), is stuff that I'm only guessing at from what I've read in other posts.
