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It was Suicune in Crystal. I started playing Yellow and then followed with Crystal, I caught Suicune with the Master Ball shortly after finding it, then maybe 10 years later I completed both games and Mewtwo was my second Master Ball catch. I've only caught 2 Pokemon in a Master Ball ever.
Dialga. I had a way of thinking that basically said, "you see this thing, this time god? It deserves the ultimate Poke Ball." I also thought it was really hard to catch, so I basically had to. Helps that Dialga was actually pretty hard to catch with normal means, so the thing saved lots of time.
Zapdos in LeafGreen! I came rather unprepared and had no balls left except for the Master Ball. I didn't know it was that rare so I used it. That Zapdos became my dearest Pokémon once I realized the worth of the Master Ball.