I used to use it on the strongest legendary in the game. However, in my SS, I saved the Master Ball cuz I believed I could catch the legendaries with any old Poke Ball. I ended up catching Raikou, Entei, Suicune, and Ho-Oh with Ultra Balls, Lugia with a Heavy Ball, Latias and Latios with Dusk Balls, and Zapdos with a Fast Ball.