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Well 'cause this can apply to more than Black and White, I'm throwing it over to PGC. Plus we've already got that one asking what you used your masterballs on.
I usually use my masterballs for the main legendary of the game. (On the front covers; Girantina, Palkia, Ho-oh, Lugia etc.) and once I've used my masterball, I just use mainly ultra balls and any other spare bals in my bag; which are often just dusk balls or heal balls.
So far in black, I used a quick ball and caught tornadus on the first shot!
I caught reshiram in a luxury ball as well as Landorus
I caught Kyurem in a dive ball (randomly chucked it lol)
I think Dusk Balls and Timer Balls always work really well. For some reason, I can't bring myself to use Great Balls, Ultra Balls or Master Balls though. :/
Well, like everything now outside of Kanto / Johto I mainly use Poké Balls (Great and Ultra balls are only for things in Kanto / Johto, where the balls originate, or pokémon I'm trading away). However, sometimes I use a Master Ball. Mainly when catching Mesprit / Cresselia when I have no desire to use it, or Mewtwo, as to me the "M" means it's for Mewtwo.
And if I'm in Hoenn / Sinnoh, I'll use one of that region's exclusive Poké Balls alongside Poké Balls. Except for the Regi Trio in Platinum - I only got them once, and I literally sold everything except my most precious tms in order to buy hundreds of Poké Balls in groups of 10 in order to get Premier Balls - Premier Balls for event legendaries, makes sense right?
Oh, did I mention Unova? Well, I'm not sure as I can't use Dream Balls, but I think it may be just plain ol' Poké Balls, or maybe a mixture of the imports from other regions. Who knows?
But yeah, I'm very specific. Gone are the days of just lobbing whatever happens to be in my bag!
It depends. For example, for Groudon I use Dark Balls. For the others, I use quick balls. After, I use ultraballs or chronoballs. But I can also use GreatBalls because I'm lucky with legandaries. I caught Rayquaza with a GreatBalls, all is possible :)
Ultra, Dusk, and Timer are my most popular choices. For a roaming legendary, like Lati@s or Thundurus, I use the Master Ball. And I've caught a few in a Pokeball once. Long ago, I had a challenge where catching Pokemon in a Pokeball was a requirement, including legendaries.
I tend to use a Quick Ball in desperate hope, then give up, wittle it down, and toss Dusk Balls if I can. If it's not in a cave or it's daytime, I bring out the ultra balls. I think I caught one of the Pixies in DPPt with a Timer Ball, though, since it had to have been over 100 turns. <_<
I usually use the master ball for the main legendary of what ever game I'm playing. I'm going to go through my PC and see what balls I used for legendary Pokemon.
Fire red
Mewtwo: Master ball
Zapdos: Ultra ball
Articuno: Ultra ball
Moltres: Ultra ball