My favourite balls, early in the game, are Pokeballs. If possible I catch all my Pokemon in these balls - I'm not sure why I do, I just find it more pleasing. Perhaps this habit comes from Ash Ketchum...
Although, when I'm attempting to complete the Pokedex, I'll use whatever balls suit me the best - generally I play at night, so I'll just use Dusk Balls all of the time, as they are 4x more effective than Pokeballs.