I upgraded to GNU/Linux Ubuntu 12.10 but have been unable to use Unity properly afterwards. Indeed, I encountered the exact same problem as a lot of people: the Unity side and top bars are not displaying, although in my case, Unity seems completely broken, as I can't even right-click. However, in my case, it's worth noticing that I have an Optimus laptop with a Nvidia graphics card (GeForce GT 540M). Bumblebee and its 'optirun' command is working just fine, as usual, after the upgrade.
I tried several things, as resetting Compiz and Unity (with the command 'setside unity') -- which works but I have to do it everytime I boot and it resets all my settings -- updating/reinstalling/reconfiguring my Nvidia drivers as well as bumblebee, trying with Nouveau drivers instead of nvidia-current, check if linux-headers-generic were installed (they were). However, I couldn't reset xorg.conf files as they're just not there. There is neither xorg.conf file, nor its backup in /etc/X11. I think this is where the problem comes from, although I'm far from an expert. Maybe retrieving a xorg.conf file will fix this mess, but I have no idea how to do that.
I'm just tired and don't know what to do. So, here I am, begging for your help.