The prefs file can be found in the following locations.
Linux
$HOME/qube/qube_guiPreferences.conf
Windows
C:\Documents and Settings\USERNAME\qube\qube_guiPreferences.conf (Windows XP)
C:\Users\USERNAME\AppData\Roaming\qube\qube_guiPreferences.conf (Vista and above)
OS X
~/Library/Preferences/qube/qube_guiPreferences.conf