According to this thread I can disable this thing altogether but this battery-critical-power-down not always happens. Is there a way or terminal command that can stop the power manager shutting down my computer when that infamous message box pops up?
nothing here and it should just crash with undetermined results if it actually ends up with an empty battery. Run
gconf-editor from command line and go to
Command line option:
gconftool-2 --set --type string /apps/gnome-power-manager/actions/critical_battery nothing
As far as i know, the computer can be set to either Shutdown, or Hibernate (free space/swap space providing).
If Hibernation is something you consider an alternative, then you should be able to change it in the Power Manager.
If not, then the system is trying to protect it's hard disks/memory from corruption, and it would be very difficult to disable, and is something i can't help with.