I pretty much nickname almost all of my Pokemon. The exception usually being Legendaries, but even then, I have nicknamed one Legendary (Zekrom) 'Raiden', because I couldn't resist. It was for naming him after the Japanese god of thunder and lightning, but it had a bonus of having the same name as an MGS character.
As for which Pokemon I've nicknamed (off the top of my head): Torterra: Tarin Infernape: Victoria (female) Haxorus: Demise (female) Floatzel: Aqua (female, after the Birth by Sleep protagonist) Samurott: Kanoro Krookodile: Shades Lucario (physical-based one): Abraham Lucario (special-based one): Aaron Arcanine: Jacob Zekrom: Raiden Typhlosion: Horatio (SoulSilver) Typhlosion: Axel (White) Blaziken: Ignacio (Emerald) Blaziken: Phoenix (White) Manectric: Kiara Rapidash: Epona Scyther: Stryker
I am a Christian, and proud of it. Common sense really isn't so common.