I nickname everything.
No, really, everything.
One of my favorite perks in the game is the ability to nickname your Pokemon. I also collect one of every single Pokemon possible and put them in national dex order in my PC box. Every Pokemon in my PC box has their own special name, and often times I will name them either based on what seems the most fitting, a memory, a special person, or a reference/joke. Its almost kinda like a miniature journal because every word I come across triggers some kind of thought when I go back and look at them. For example:
Specs the Kecleon (named after my actual pet chameleon)
Paddle and Danda the Oshawott and Pikachu (after my mystery dungeon characters, I have several like these)
Jay the Raichu (after a close friend)
Tecton the Whiscash (plate tectonics, fitting)
Teemo the Paras (hehe)
Charzi the Charizard ( a lame name I know, but its after my original very first Pokemon ever that I no longer have. :c)
Tomo and Dachi the Plusle and Minun (me and a friend had P+M plushies nicknamed this)
Tony and Maria the male and female Nidoran (from the old anime episode of the Nidoran)
Somber the Umbreon (fitting)
And for X and Y, you can bet I'm probably going to nickname my Fennekin evolutions Kinvix and Pyrokinen.
My only exceptions for not nicknaming a Pokemon are for tradebait, and the ones that can't be nicknamed (events, this bothers me so much because now I cant have Petunia the Shaymin, Miku the Meloetta, or d'Artagnan the Keldeo.)
Yeah I know I'm lame. /end dramatic nicknaming ramble