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You can use it on whatever you prefer really. Though I personally don't use it at all unless I'm really struggling with catching a legendary. I used mine on Mewtwo.
I personally, deployed it upon Mewtwo, but only because the colour scheme of the Master Ball goes well with Mewtwo and only Mewtwo. I mean it does have that glaring 'M' on the ball itself. Everything else get's Luxury balls chucked at them until they feel pampered enough to clamber up inside.
Mewtwo has the lowest catch rate (I think) so definitely that's what I would use it for... if I wasn't lazy and just used it on the box legendaries so I could get on with the story, haha.
I used mine on Rayquaza because I didn't have many other poke balls available, not to mention I forgot to save before Rayquaza's appearance. :pink_blush: Mewtwo would have been a better choice in my opinion though, as I really like it when the color scheme of a pokemon matches the colors of the ball.
//Edit: And I just now notice that this is the XY section and I was talking about my master ball usage in OR. My bad. And there's no Mewtwo there. Double bad.
In X though, it seems I still have my master ball and I've already caught all the legendaries that are available.
I used mine on Mewtwo, with the intent of banking it and using bottle caps on it. Was after Living Dex and could not be bothered to go through catching in regular ball (Master Ball fits colours too IMO0
I caught most of the main legends in Ultra Balls/Quick Balls so I ended up saving the Master Ball. I don't have that save anymore, but I probably would have held it off for either a shiny or one of the extremely difficult remaining legendaries with a low catch rate.