Aside from the first/second gen games, and my original playthrough of Sapphire (which I used it on Latias), I don't use the Master Ball. In fact, I've saved all of the ones I've gotten and moved them over to Heart Gold where I currently have 5 in my bag.
After an unfortunate encounter with a Shiny Paras, I've decided that the only time I'll use a Master Ball is if it's a Shiny Pokemon (unless it's under level 15, then I might try a few Ultra Balls, and then throw a Master Ball if those don't work).