Old post, but new people may like the idea:
In Soul Silver, I used my Master Ball to catch Entei. I wanted him for the Elite Four, but didn't have patience to travel everywhere looking. It was worth it because he always flees or uses Roar (after I use Mean Look), taking forever to catch him. I wanted a good Fire type for the Elite Four since I chose Chikorita to start with, and I didn't need Raikou because I had Ampharos.
Most folks use their Master Ball for Lugia, but with a little skill, a dozen Hyper Potions, and a lot of Ultra Balls, Lugia is not that difficult to catch. I actually caught him with a Net Ball if I remember correctly.