Well... Not too often... I ALWAYS make it a point to nickname my starter its final form (like naming a mudkip swampert). Mostly, cuz it has some interesting effects when evolving... (like Congratulations! Your Typhlosion evolved into Quilava!) also, when i'm breeding Pokémon or natures, i usually name the desired ones by their natures (so i have a Tyranitar called adamant, and another called mild). Sometimes, when i'm really bored, i name them after my friends... :-/
Oh yeah, sometimes i also give nicknames which are kinda similar to the original name. (Ziggy to a baby Zigzagoon, Dumbell to Beldum, Batty to Crobat etc...)