How do you use your Master Ball?

[Elite Overlord LeSabre™]

Mewtwo in the first game, roaming Pokemon in all the others. Unless I see a shiny that I can't battle to the point where I can capture it or runs away/selfdestructs, but I haven't had to use a Master Ball on a shiny yet.

Sometimes I don't use the Master Ball at all and start hoarding them by trading them to one of my main game versions (Platinum/ Leaf Green)

 

[BHwolfgang]

I usually save it for a Legendary Pokemon, preferably one that is level 70. It takes me a much longer time capturing Mewtwo than it does capturing a roaming Pokemon. Also, it doesn't take much effort encountering a roaming Pokemon if you tend to explore a lot. I usually capture one between the first and fourth time seeing that particular roaming Pokemon. However, there was that time when I captured an Emolga with a Master Ball while playing my friend's Pokemon Black....

✈ Mewtwo in R/B/Y
✈ Lugia in Gold
✈ Ho-Oh in Silver
✈ Rayquaza in R/S/E
✈ Raikou in SoulSilver

Hmm... yeah, I didn't use the Master Ball in Platinum. Raikou was being really annoying, so I just wasted it on my seventh encounter. Entei was extremely easy; I just threw a Fast Ball.