I don't know about you, but I'm using the C.Falco PPA in Ubuntu and the way they set up the defaults is a little bit confusing because you don't always have write permissions to the directories outside of your /home/. To avoid all these problems my /etc/mame/mame.ini file only has one line in it:
That way it always points to the .mame directory in my home.
Another trick I've learned is don't mess with the defaults for hashpath, fontpath, plugins, or languagepath. The files in those directories are version dependent and everything gets screwed up if you have those directories pointing to something that doesn't get updated with each release. Copy over those paths over from the /etc/mame/mame.ini file.
One final trick since I've started using the default UI more these days; rename the /etc/mame/ui.ini file to something else, and then create a new ui.ini file under your /home/xxx/.mame/ directory and use that file to define all of your UI search path options.