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Whatever I feel like using at the time. Throughout the game, I tend to use whatever I have the most of first, while once I can afford plenty of Ultra Balls I use those to capture whatever I want. Those that find their way onto permanent teams get captured in whatever ball I think matches their design the best. Overall, I still think the Great Ball looks best, though.
I always buy Pokeballs in quantities of 10; then, I sell back the pokeballs. I may start a thing where I only use Premier Balls for capture. That'd be expensive though, and it'd only be for show. (It'd essentially 1000 for each ball.)