I especially like the Projectile Ball, the Advantage Ball, and the Honey Ball.
Maybe a ball you could customize to when you catch the Pokemon, some TM's or HM's are automatically taught to the Pokemon or something.
Or a ball that automatically levels a Pokemon when you catch it, like a 1 level ball would cost 1000 a 2 level ball would cost 2500, a 10 level ball would cost 15000, or something along those lines.
A ball that automatically makes the caught Pokemon shiny. 0_o that would be awesome.
Or just a ball that is a normal Pokemon Ball but instead you could pick the color or design of it.
There could be a ball that when thrown puts the Pokemon to sleep.
Maybe a ball that evolves the Pokemon instantly.
A ball that makes the Pokemon and happy and makes the said Pokemon like the trainer.
A ball that automatically stores the Pokemon into the daycare center.
These are just some of the ideas I thought of on the spot, that probably won't come into the game.