Nautilus doesn't work.... from command or from unity

This problem is probably stemming from the fact that you uninstalled GNOME 3. I don't know what version of Ubuntu you are running, but I know in version 12.10 Ubuntu actually shipped with an older version of Nautilus than the most recent GNOME version.

Regardless, you must have switched Nautilus versions somewhere through the upgrade and some important files were lost

My best recommendation without fully understanding the system would be to simply purge and reinstall Nautilus.

This can be done with the following commands:

sudo killall nautilus - this will make sure you kill the Nautilus program before you start working with it.

sudo apt-get remove --purge nautilus - this will totally remove Nautilus and any residual config files.

sudo apt-get update - this will make sure your sources are recent.

sudo apt-get install nautilus - this will freshly install Nautilus again.

Sources:

http://www.omgubuntu.co.uk/2012/08/ubuntu-12-10-will-ship-with-older-version-of-nautilus https://launchpad.net/ubuntu/+source/nautilus/1:3.5.90.really.3.4.2-0ubuntu1/+build/3739314