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I can't remember ever using a master ball on a legendary, I've got three at the moment on Diamond (one from fire red and one from emerald) that I'm saving for Shaymin, Darkrai and Arceus when the events finally come to Britain.
I play through every game at least ten times, and collect the better items to trade over to my main game, my 'base of operations.' Then I catch the Legendaries on only one or two games. So, I never run out of Master Balls.
I always get a Masterball in the lottery in every game, even on those of my friends, so now I have about 8 Masterballs left, WITHOUT restarting.
Things I used them on:
Yellow: Articuno and nothing.
Silver: Entei, Suicune.
Emerald: Rayquaza, transferred 7.
Diamond: Dialga, Mesprit, Cresselia, Heatran, Regigigas, Giratina, Gible(I was so happy after 17 hours of searching, I just caught it and it appeared to have the right Nature and good IV's, so I trained it too!) and Rotom.
Well, supposing I caught some legendaries (those who don't run away) without using the Master Ball, I'd probably use it to a Legendary that often runs away. I already used my M. Ball to Cresselia in Diamond, so I might have a hard time catching Mesprit. x_X
Otherwise, if not a legendary, I'd probably use it to a shiny & rare Pokemon.
I hold it for a shiny i use ultra balls on legends but if i dont find a shiny i trade it to the next gen if i can or have a pokemon hold it in the box/storage games till I restart my game so i always have it for them