Don't use it to any pokémon, it's easy to catch em all without using masterball. I have throwed Master Ball only one or two times and I think it's not funny ball. I have all pokémon in my Gold save game and haven't used Master Ball. Dogs were hard to catch but they can be captured by Ultra Balls. I think I caught first Entei (Ultra Ball), then Raikou (Ultra Ball too) and Suicune was hardest at that time but then I threw it with Great Ball and it was caught. Ho-oh and Lugia is easy to catch, sometimes I have had them by just throwing one Ultra Ball at the beginning of the battle... I personally don't use Master Ball but if you really want to use it, use it to a dog.