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Well, you don't really need to use it on anything. All the Pokemon in there can be caught without the Master Ball.
My main suggestion would be for either Mesprit or Cresselia since those two run around Sinnoh, forcing you to search and hunt them down and then Mean Look to keep them in battle etc... but they don't necessary need the Master Ball for them to be caught. They're just probably the most annoying to catch in the game.
Otherwise, save it for like a shiny later or something else rare.