I totally intentionally use Pokeballs to match colors/give a stark color difference. Pink Pokemon, Pokemon with feminine qualities, and Pokemon that are capable of healing are caught in Heal Balls. Hence, Audino are always in Heal Balls for me, as are Pidoves (the heart), Petilils (feminine Lilligant), etc..
I'll use Net Balls on Water-types, but for Bug-types, I'd rather use the Nest Ball, unless the Bug is blue. For Water-types, anything could really go in the Net Ball, but if I have to choose between a Net Ball and a Dive Ball, I choose the Dive Ball. General evolved Pokemon in the wild will be caught in Great Balls (or, occasionally, Ultra Balls). Only Dark-types are usually caught in Dark Balls, sometimes Ghost-types. Everything else I try to catch in a Pokeball, and I like to keep the majority of my team in Pokeballs.