Actually, my brother has like, twelve Masterballs in his Pokemon White 2 version *he hasn't obtained his in White 2 yet*. It started with trading a Pokemon that held the Masterball from his ruby to his sapphire. Trading two Pokemon that held the two Masterballs to his Firered. Trading three Pokemon that held the three Masterballs to his Leaf-Green. Pal-parked all four Masterball carrying Pokemon to his Diamond Version. Traded five Masterball wielding Pokemon to Pearl. Six to Platinum, Seven to HeartGold, Eight to Soulsilver. Transferred Nine to Pokemon White. Traded Ten to Pokemon Black. Traded Eleven to Pokemon Black 2, and finally traded all twelve over to his White 2, where he will soon gain his Thirteenth.
All in all, he could develop two teams with all of the ones he has currently. It is possible, just time consuming. He probably won't ever use them either :P .
As for me, I used to use it for Roamers, or Mewtwo in Firered. However, I have recently slowed up on using the Masterball, and much like my brother, keep it for collection purposes.