The BNC connectors are most likely RGB inputs. These can be very useful. NickG and Snaake both use NEC multi scan computer monitors. The RGB inputs can be used for hooking up real arcade inputs such as Jamma. I know NickG has a jamma setup hooked up to his.
I don't know whether or not there would be any advantage to hooking up your mame pc via RGB instead of the VGA inputs, but I am interested to find out as I also have one that will be going in my cab. If there isn't any advantage of hooking up the pc via the RGB inputs, I would like to hook up my PC via the VGA and have a Jamma setup on the RGB's. I am interested to see if any other good info on this gets posted here.