EDIT: non gnome applications(like firefox) run without any problems.
If you are not working as root all the time
if you where in your HOME directory (as you normally are when you open a terminal/command-line)
you would have damaged things inside your HOME directory.
If you where "root"
if you where in some system direcrory - you damaged this one instead.
Was the command: rm -fr ./*
The one you posted is only a part and will not do anything as it is.
You should be able to get a clean state by:
- logging out of Gnome
- go to a console (CTRL+ALT+F2)
- log in there and remove the ./.gnome2 ./.gconf and ./.metacity directories
- go back (ALT+F7) and log in
all the missing and possibly corrupted configuration directories will be recreated