First off I have to make sure I have enough 'balls' with me (Pokeballs, Great Balls, Ultra Balls, any other given or found along the way).
I save before legendaries too.
I try to lower HP as low as possible (except for my only shiny - instant master ball)
If its a Pokemon I really want, I'll have my Watchog (or equivalent in other earlier generation games) use Mean Look (another similar move to prevent Pokemon from escaping in earlier generations).
I'll use which ever ball seems most likely to catch the Pokemon if I have one (dusk ball, net ball, etc..) other wise I'll start with Pokeballs for common Pokemon or lower level Pokemon. Great Balls for mid level Pokemon (around 30 to 50), and Ultra Balls for legendary and higher level Pokemon.... I'll use the others too if I run out of a certain ball.
Guess I'm not different from many other trainers.