It depends on the specific version you are playing. In some games there are glitches (like in emerald) where you can duplicate pokemon and items. So I would replicate it if you can.
What pokemon should I save my Master Ball for?
I'd save it for giratina, but if you already have him then go for heatran, because it's far more useful then regigigas, but both regigigas and heatran have the same catch rate of 3% so i'd also recommend using it if you have tried to catch one of them and it isn't working