So this is a fun problem. After upgrading to Raring Ringtail, the open file command for nautilus on everything except the file browser in unity itself (opening downloads from browsers, clicking on removable media in unity) opens the Disk Usage Analyzer instead of nautilus. Is there a config file somewhere that chooses these defaults? I can't seem to find it.
To me it seems the appropriate way is to define Nautilus as the default application to handle the mimetype inode/directory. This can be done via console with
xdg-mime default nautilus.desktop inode/directory
What it does is adding the following line to .local/share/applications/mimeapps.list
About accepted answer: I don't know what adding a colon and a number to the mimetype in the baobab desktop file does, but if it's just disabling the unwanted behaviour this won't be sufficient. I can imagine another application hijacking/overriding the mimetype assocation again.
Another point is that you have all your defaults defined in one place.
Open the file
/usr/share/applications/baobab.desktop by issuing this command:
gksudo gedit /usr/share/applications/baobab.desktop
And remove this line:
Then save. If that fixes your problems, please take a minute to file a bugreport on Launchpad.