I haven't used my Master Balls yet, and probably won't too soon anyway. I've caught almost all the legendaries, usually with Dusk Balls or Ultra Balls, a Timer Ball for Cobalion and a random Quick Ball for Uxie. I actually liked chasing after the roaming Thundurus in White, and even though I did get a bit annoyed when I realized it can flee while sleeping (why?!), I still didn't use the Master Ball.
I probably will use it on a shiny though, when and if I ever encounter one in the wild