I still have 2 Master Balls... I don't have Genesect, but I know I can't get him any more.
I have both Zekrom and Kyurem.
What should I do with the Master Balls?
Once you have caught all the legendary Pokemon, there isn't much you can do with Master Balls. So here are my suggestions:
Make sure you have actually caught all the legendary Pokemon. In Black 2, as well as being able to catch Zekrom and Kyurem, you can also catch Regirock, Registeel, Mespirit, Uxie, Azelf, Cresselia, Heatran, Cobalion, Virision, Terrakion and Latios.How to catch all legendary Pokemon in Black 2.
If you have caught all those, then you could chain fish for a shiny Pokemon, and use a Master Ball on that, because shiny Pokemon also look cool in Master Balls.
If you can't be bothered to chain fish, or you find it hard, you could always just use your Master Balls on wild Pokemon. But at least use them to catch Pokemon you think you will actually use at some point.
Or, since there isn't much to use them on, you could always move all your good Pokemon to another game, and new game Black 2, and catch the legendary Pokemon you were planning to catch this time.
And if you have Pokemon X or Y, you could catch a Pokemon in one of those Master Balls, transfer it to X/Y, and breed it with another Pokemon. Because in X and Y, the baby of two Pokemon will be in the same Pokeball as the mother, even if you only have one of that Pokeball. So you could do that with your Master Balls, even though it won't count as actually owning more Master Balls.
I hope this helps!