I only name my Pokemon when they have a very specific use case. For instance, my family and I are working through the entire first 7gens on our hacked ds'. Personally I'm doing so with gengar line as my starter as I've always wanted to do that. I've named her after the Greek Godess of Witchcraft and dreams, Hecate due to my love of the hypnosis/dream eater/nightmare abilities. I gave myself a Mew as an HM dump and named him Gumby for being so adaptive.

Outside of these two, I've yet to find another Pokemon to keep permanently so I don't plan to name any of them.