I let my brother play my Diamond game. He used my masterball on a bibarel. I've hated them since tha day. Especially since there are TWO running legendaries now.
He also catches random weak pokemon for his own teams and I often find the ds on with the only pokemon I caught myself in my team being my staraptor because it can fly...but that's off topic.
i accidentally used it on a haunter, forgot about it (as i was going to face koga, and so then decided to fight him before resetting so i wouldnt be surprised by anything), and saved. then i realized that i had wasted my master ball, so i restarted my game <(;_; )> <-- me being sad
I once, on Blue, caught Zapdos with it. I know it doesn't sound really stupid, but it was the stupidest thing I ever did with a masterball. Now I always keep my masterball in the PC so I don't accidentally use it, or if the game doesn't allow ball storage, I make a Pokemon hold it, do it doesn't appear in my bag.