In Sapphire which Pokemon should use the master ball on?

I would recommend that you use on latiOS or latias w/e which they are because raquaza and kyogre are fairly easy to catch

You don't have to use your Master ball on anything. You can use it on Kyogre, but that's the easiest legendary to catch, so I don't recomend it. You could save it for later on, like for Rayquaza. That's MUCH harder to catch! It's at level 70 when you encounter it, but you could still catch it with a normal Pokeball (I did). And then, you could catch Latias with it, which would be the best in my opinion, because unless you have a Pokemon like Wobbufett, with the ability Shadow Tag that doesn't let the opponent escape from battle, then it would be pretty hard to catch. So I say catch Latias with your Master ball.