In most games, I nickname about 25-30% of my Pokemon, just based on which ones I care to name or can think of a good name for. However, recently, with a couple of my monotype challenges, and with my Black and the White I just rented, I have nicknamed every single Pokemon on them. Obviously, over time, this affects the quality and originality of the nicknames, but there's something to be said for choosing names anyway.
I like when people nickname their Pokemon. It livens the game up and gives the Pokemon their own personalities, with somewhat of a reflection of the OT. One time on the GTS I got a Feebas with a dirty word as a name (I won't post it here for the adverse possibility of me getting banned or, at least, my post being removed); while a little immature, it was better than nothing.